The former England spinner represented the county for 23 years as a player and joined the coaching staff following his retirement, taking the top job in 2016.
He has been unable to bring success to the SWALEC Stadium, though, and departs after winning just two Specsavers County Championship matches in 2018.
The club will name a successor after appointing a new director of cricket.
Chief executive Hugh Morris said: "It was an incredibly difficult decision for the board to make, but given our performances in the County Championship we feel it is the right time for a change.
"Robert is always welcome back at the club and we hope he will continue to act as an ambassador for Glamorgan and Welsh cricket.
"He is one of our greatest players and the most successful player we have ever had at the club at international level and has done more than anyone to promote not just cricket in Wales, but Welsh cricket to the world."
In 2017 the 48-year-old led the team to a first Twenty20 finals day in 13 years but, despite earning praise for blooding locally produced players, he could not reverse a poor sequence of results with limited resources.
"Although our County Championship campaigns did not go as I would have liked, we were able to compete admirably in the shorter formats of the game with a small and young squad of players," he said.
"Glamorgan will always hold a big piece of my heart and I would like to wish the club and supporters well for the future."
Morris added: "On behalf of the club I would like to thank Robert for the incredible contribution he has made to Glamorgan, not just as head coach but also as a player, assistant coach and ambassador over the last 30 years.
