The Robins currently sit bottom of the table with Millen’s fate being sealed by a crushing 5-0 defeat to Blackpool on Saturday.
His departure ends a 12 year affiliation with the club after ending his playing career at Ashton Gate in 2003.
Prior to becoming manager in August 2010 Millen was in charge of the club’s youth team and also served as an assistant manager under Brian Tinnion, Gary Johnson and the man he succeeded Steve Coppell.
Millen’s tactics have been under particular scrutiny this season after he failed to stray from his preferred 4-5-1 formation even when the side were bereft of both goals and confidence.
Chairman thanked Millen for his years of great service to the club and also confirmed former Southampton manager Steve Wigley will take charge of training while the search for a successor gets underway.