The 21-year-old has signed a two and a half year deal at the club where he was on loan last season.
Stevenson played 13 games for the club last term, scoring two goals.
Now he will be back with the team where he hopes to play regular football.
Stevenson has been with Wolves since 2014, but never managed to break into the first team on a regular basis.
Director of football Tony Humes said to the Colchester website: "He is someone who fitted in very well last season."