Thomas started his career with Chiefs in League One in 2003, before moving to Premiership side Gloucester in 2005.
The 34-year-old also had a spell with Bristol before rejoining Exeter in 2009, helping them win promotion to the Premiership in the 2009-10 season.
He will stay with the club in an unspecified role with the academy side following his retirement.
"Being part of the Chiefs journey out of the Championship and then into the Premiership, where we've really established ourselves as a club has been amazing," he told the club website.
"What I've achieved, especially here at the Chiefs, is something I'm very proud of.
"To get to do a job that you love every day, working alongside some of your best friends, I don't think you can't really ask for any more than that."
Exeter are second in the Premiership table ahead of the final game of the season, already assured of a place in the play-offs.
Exeter Chiefs scrum-half Haydn Thomas will retire at the end of the season after 211 appearances for the club.