In Naked City's characteristic early style, songs were often performed at astonishingly fast tempos, drawing heavily on thrash metal and hardcore punk's emphasis on extreme speed. Many songs were quite brief, and typically switched musical genres every few measures, perhaps comparable to spinning a radio dial at random and hearing the same band performing on every station. One critic described Naked City's music as "jump-cutting micro-collages of hardcore, Country, sleazy jazz, covers of John Barry and Ornette Coleman, brief abstract tussles — a whole city crammed into two or three minute bursts." This fast-change tendency was inspired in part by Carl Stalling — a Zorn favorite — who wrote music for many Warner Brothers cartoons (featuring Road Runner, Bugs Bunny, Daffy Duck and others); music that featured frequent shifts in tempo, theme and style.
Naked City's eponymous first album was distributed by Elektra Nonesuch and featured a famous Weegee photograph (taken 1943) of a dead gangster on its cover along with macabre illustrations by Maruo Suehiro. There was disagreement between Zorn and the label over cover art on subsequent albums. Zorn wanted to use explicit S&M pictures, images from 19th century medical archives, and execution photographs, most notoriously of a Leng Tch'e victim; Elektra Nonesuch refused. Zorn ended his relationship with Elektra, releasing subsequent Naked City albums on Shimmy Disc and his own Avant and Tzadik labels.
Naked City varied their stylistic approach on later releases. The cover repertoire was expanded to include pieces from various modern classical composers such as Alexander Scriabin, Claude Debussy, Charles Ives, and Olivier Messiaen, whose works are featured on the album Grand Guignol. Leng T'che featured a single piece, over 31 minutes in length, of gruelingly slow heavy metal. Torture Garden was made up of several "hardcore miniatures," and Absinthe was ambient and noise textures.
Naked City found perhaps their greatest following among the fans of the many death metal, metal and grindcore bands with which they performed, such as Blind Idiot God, Napalm Death, Carcass and Live Skull. The appearance of "Osaka Bondage" - taken from the album "Torture Garden" - on the Earache sampler Grindcrusher II helped this to some extent.
Zorn discontinued Naked City after Absinthe when he felt "... the need to write music for other ensembles, in other contexts, with new ideas." A brief reunion occurred in 2003 for a few shows at European jazz festivals.
Filmmaker Henry Hills completed Heretic short film about Naked City and documented John Zorn, Christian Marclay and Fred Frith activities. The films were screened France in festival Vidéo Formes and by curator Jérôme Lefèvre in a program about New-York Avant-Garde in both Cinema and Music.