The band's style of alternative rock music is heavily influenced by punk rock|punk and indie rock, and while highly melodic, is capable of being tremendously abrasive at the same time. Francis is the Pixies' primary songwriter and singer and has a distinctly desperate, yowling delivery. He has typically written cryptic songs about offbeat subjects, such as unidentified flying objects|UFOs and surrealism. References to mental instability, violent bible imagery, and physical injury feature in many of the band's songs.

The group is frequently posited as the immediate forebear of the alternative rock boom of the 1990s, though they disbanded before reaping any of the benefits this might have brought them. Avowed fan Kurt Cobain's acknowledgement of the debt Nirvana owed to the Pixies, along with similar tributes by other alternative bands, ensured that the Pixies' legacy and influence grew substantially in the years following their demise.