The music video for "Bones" marks the music video directing debut of film director Tim Burton. Clips of the band were shot August 17–18, 2006, and were edited together along with CGI backgrounds and characters, including a (fitting) Burton staple: skeletons. Michael Steger and Devon Aoki star in the video.
Scenes from the films Lolita, Creature from the Black Lagoon, and Jason and the Argonauts, more specifically the scenes with Ray Harryhausen's skeleton-men, are shown behind the band. There is a sequence where Flowers's hand is replaced with that of a skeleton. The beach scenes from From Here to Eternity and 10 are recreated with skeleton figures. The leading couple are seen driving onto the beach where the girl removes her hair to reveal her skull and the man pulls off his shirt to reveal his skeleton. The two leading skeletons are later seen running across the beach to embrace only for them to crash into one another and shatter to pieces. Then on the beach a wave comes over to reveal the two skeletons kissing. At the end of the video, the entire band are skeletons, and they all fall apart at the song's final note.
The drive-in depicted unofficially is that of the West Wind Las Vegas Drive-In Theatre located in North Las Vegas, NV.
At the 2007 Shockwaves NME Awards it won the award for Best Video.