Jonathan was born in Texas. He attended Westbury High School in Houston, Texas. He has suffered from a dissociative disorder called depersonalizaion, since age 12.

Jonathan is the award-winning director of Tarnation (2003) and the forthcoming All Tomorrows Parties (2008) about the cult music festival. As an actor, Caouette played a major role in the 2006 film Fat Girls and is set to star in the forthcoming Portland (2008). He also appeared in Shortbus, directed by John Cameron Mitchell.

He lives in New York City with his partner David, his mother Renee, and his grandfather Adolph. His 11-year-old son Josh, who co-starred in the documentary Bi the Way, lives in Texas with his mother.