The song is one of the most well-known of The Who's recordings. It starts off with a solo voice singing over an arpeggiated guitar, later adds in bass guitar and ethereal harmonies, eventually breaks out into full-scale rock anthem when a second theme is introduced near the end, and wraps up by a brief reprise of the quieter first theme. Songs written in alternating sections were something of a trademark of Townshend's writing of the period, going back at least to Tommy, where it was used in "Christmas" and "Go to the Mirror!" The guitar riff at the end of the rock anthem section is also used after the bridge during the song "Won't Get Fooled Again," perhaps serving as a link between the two songs when Who's Next was intended to be a rock opera. (Some musical themes from Tommy and Quadrophenia appear in multiple places.)
The lyrics are a first-person lament from a man in the Lifehouse story, variously identified as 'Brick' or 'Jumbo', who is always angry and full of angst because of all the pressure and temptation that surrounds him, and the song was intended to be his "theme song" had the project been successful. (The lyrics of the rocking section near the end were actually written by Townshend as a prayer when he was a disciple of Meher Baba after being tempted by a groupie, and incorporated into the song when it was written.) In the incarnation of Lifehouse that was officially released as a part of Pete Townshend's solo box set, The Lifehouse Chronicles the song's meaning changes to the theme song of the story's protagonist, Ray.
The version of "Behind Blue Eyes" on the original Who's Next album was actually the second version the band recorded; the earlier version appears as a bonus track on the remastered CD release, which features Al Kooper on Hammond Organ. Pete Townshend has also recorded two solo versions, one (the original demo of the song) was featured on the Scoop album. The demo along with a newer recording of the song featuring an orchestral backing was featured in The Lifehouse Chronicles.