Despite his achievements as a professional military academic, Cui is best known in the West for his "other" life in music. As a boy in Vilnius he received piano lessons, studied Chopin's works, and began composing little pieces at fourteen years of age. In the few months before he was sent to Petersburg, he managed to have some lessons in music theory with the Polish composer Stanisław Moniuszko, who was residing in Vilnius at the time. Cui's musical direction changed in 1856, when he met Mily Balakirev and began to be more seriously involved with music.

Even though he was composing music and writing music criticism in his spare time, Cui turned out to be an extremely prolific composer and feuilletonist. His public "debut" as a composer occurred 1859 with the performance of his orchestral Scherzo, Op. 1, under the baton of Anton Rubinstein and the auspices of the Russian Musical Society. In 1869 the first public performance of an opera by Cui took place; this was his William Ratcliff (based on the tragedy by Heinrich Heine); but it did not ultimately have success, partially because of the harshness of his own writings in the music press. All but one of his operas were composed to Russian texts; the one exception, Le flibustier (based on a play by Jean Richepin), premiered at the Opéra - Comique in Paris in 1894 (twenty - five years after Ratcliff), but it did not succeed either. Cui's more successful stage works during his lifetime were the one act comic opera The Mandarin's Son (publicly premiered in 1878), the three act Prisoner of the Caucasus (1883), based on Pushkin, and the one act Mademoiselle Fifi (1903), based on Guy de Maupassant. Besides Flibustier, the only other operas by Cui performed in his lifetime outside of the Russian Empire were Prisoner of the Caucasus (in Liège, 1886) and the children's opera Puss in Boots (in Rome, 1915).

Cui's activities in musical life included also membership on the opera selection committee at the Mariinsky Theatre; this stint ended in 1883, when both he and Rimsky - Korsakov left the committee in protest of its rejection of Mussorgsky's Khovanshchina. During 1896 - 1904 he was director of the Petersburg branch of the Russian Musical Society.

Among the many musicians Cui knew in his life, Franz Liszt looms large. Liszt valued the music of Russian composers quite highly; for Cui's opera William Ratcliff he expressed some of the highest praise. Cui's book La musique en Russie and Suite pour piano, Op. 21, are dedicated to the elder composer. In addition, Cui's Tarantelle for orchestra, Op. 12, formed the basis for Liszt's last piano transcription.

Two personalities of direct significance for Cui were women who were specially devoted to his music. In Belgium, the Comtesse de Mercy - Argenteau (1837 – 1890) was most influential in making possible the staging there of Prisoner of the Caucasus in 1885. In Moscow, Mariya Kerzina, with her husband Arkadiy Kerzin, formed in 1896 the Circle of Russian Music Lovers, a performance society, which began in 1898 to give special place to works by Cui, among those of other Russian composers, in its concerts.

In such a long and active musical life as Cui's there were many accolades. In the late 1880s and early 1890s several foreign musical societies honored Cui with memberships. Shortly after the staging of Le flibustier in Paris, Cui was elected as a correspondent member of the Académie française and awarded the cross of the Légion d'honneur. In 1896 the Belgian Royal Academy of Literature and Art made him a member. In 1909 and 1910 events were held in honor of Cui's 50th anniversary as a composer.

Cui married Mal'vina Rafailovna Bamberg (Мальвина Рафаиловна Бамберг) in 1858. He had met her at the home of Alexander Dargomyzhsky, from whom she was taking singing lessons. Among the musical works Cui dedicated to her is the early Scherzo, Op. 1 (1857), which uses themes based on her maiden name (BAmBErG) and his own initials (C.C.), and the comic opera The Mandarin's Son. César and Mal'vina had two children, Lidiya and Aleksandr. Lidiya, an amateur singer, married and had a son named Yuri Borisovich Amoretti; in the period before the October Revolution Aleksandr was a member of the Russian Senate.

Because of rules related to his status in the Russian military, in the early years his musico - critical articles had to be published under a pseudonym; in Petersburg musical circles, however, it became clear who was writing the articles. His musical reviews began in the St.Petersburg Vedomosti, expressing disdain for music before Beethoven (such as Mozart) and his advocacy of originality in music. Sarcasm was a regular feature of his feuilletons.

Cui's primary goal as a critic was to promote the music of contemporary Russian composers, especially the works of his now better known co-members of The Five. Even they, however, were not spared negative reactions from him here and there, especially in his blistering review of the first production of Mussorgsky's Boris Godunov in 1873. (Later in life Cui championed the music of this late colleague of his, to the point of making the first completion of Mussorgsky's unfinished opera The Fair at Sorochyntsi.)

Russian composers outside of The Five, however, were often more likely to produce a negative reaction. This derived at least partly from distrust of the western style conservatory system in favor of the autodidactic approach that The Five had practiced. Cui lambasted Tchaikovsky's second performed opera, The Oprichnik, for instance; and his stinging remarks about Rachmaninoff's Symphony No.1 are often cited. (Fortunately for posterity, both works have survived their unfavorable premieres.)

Of Western composers, Cui favored Berlioz and Liszt as progressives. He admired Wagner's aspirations concerning music drama, but did not agree with that composer's methods to achieve them (such as the leitmotif system and the predominance of the orchestra).

Late in life Cui's presumed progressiveness as espoused in the 1860s and '70s faded, and he showed firm hostility towards the younger "modernists" such as Richard Strauss and Vincent d'Indy. Cui's very last published articles (from 1917) constituted merciless parodies, including the little song "Гимн футуризму" ("Hymn to Futurism") and "Краткая инструкция, как, не будучи музыкантом, сделаться гениальным модерн-композитором" ("Concise Directions on How to Become a Modern Composer of Genius without Being a Musician").

Cui composed in almost all genres of his time, with the distinct exceptions of the symphony and the symphonic poem (unlike his compatriots Balakirev, Borodin, Mussorgsky and Rimsky - Korsakov). By far art songs constitute the greatest number of works by Cui; these include a few vocal duets and many songs for children. Several of his songs are available also in versions with orchestral accompaniment, including his Bolero, Op. 17, which was dedicated to the singer Marcella Sembrich. Some of his most famous art songs include "The Statue at Tsarskoye Selo" ("Царско - сельская статyя") and "The Burnt Letter," ("Сожжённое письмо"), both based on poems by Cui's most valued poet, Alexander Pushkin.

In addition, Cui wrote many works for piano and for chamber groups (including three string quartets), numerous choruses, and several orchestral works, but his most significant efforts are reflected in the operas, of which he composed fifteen of varying proportions. Besides children's music (which includes four fairy tale operas as well as the aforementioned songs), three other special categories of compositions stand out among his works: (1) pieces inspired by and dedicated to the Comtesse de Mercy - Argenteau (whom the composer knew from 1885 to her death in 1890; (2) works associated with the Circle of Russian Music Lovers (the "Kerzin Circle"); and (3) pieces inspired by the Russo - Japanese War and World War I.

As to the current status of Cui the composer, in the last few decades one of his children's operas (of which he composed four) entitled Puss - in - Boots (from Perrault) has had wide appeal in Germany. Nevertheless, despite the fact that more of Cui's music is being made available in recent years in recordings and in new printed editions, his status today in the repertoire is considerably small, based (in the West) primarily on some of his piano and chamber music (such as the violin and piano piece called Orientale (op. 50, No. 9)) and a number of solo songs. The received wisdom that he is not a particularly talented composer, at least for large genres, has been cited as a cause for this state of affairs; his strongest talent is said to lie in the crystallization of mood at an instant as captured in his art songs and instrumental miniatures. Although his abilities as an orchestrator, too, have been disparaged (notably by his compatriot Rimsky - Korsakov), some recent recordings (e.g., of his one act opera Feast in Time of Plague, from Pushkin) suggest that Cui's dramatic music might be more interesting to pursue with regard to this feature.

Cui's works are not so nationalistic as those of the other members of The Five; with the exception of Pushkin, his operas do not display a strong attraction to Russian sources. In the area of art song, however, the vast majority of Cui's vocal music is based on Russian texts. Overt attempts at Russian "folk" musical style can be detected in passages from his first act of the collaborative Mlada (1872), The Captain's Daughter, a couple of the children's operas, and a few songs; many other passages in his music reflect the stylistic curiosities associated with Russian art music of the 19th century, such as whole tone scales and certain harmonic devices. Nevertheless, his style is more often compared to Robert Schumann and to French composers such as Gounod than to Mikhail Glinka or to Cui's Russian contemporaries.