Radford joined the Welsh county after leaving his role as batting coach with West Indies in October 2013.
Glamorgan finished fourth in Division Two of the County Championship in 2015.
"I am pleased the team showed major improvement in the past two seasons. It is disappointing for me not to be able to see the work through to its conclusion," said Radford.
Glamorgan chief executive Hugh Morris praised Radford, adding: "His hard work and commitment to the role has been evidence for all to see and under his leadership we have made an important step forward".
The club have made no comment about a potential replacement, but it is understood that bowling coach Robert Croft will lead pre-season training.
Toby Radford has left his position as head coach of Glamorgan a year before his contract was due to end.