The Zimbabwean, who had been in charge since 2009, found his position under increasing pressure after England suffered heavy defeats in the test series and he is now set to be given a new role with the national academy in Loughborough. (Agencies)
"Following the recent very disappointing Ashes defeat it is clear to me that this is now time for England cricket, led by (captain) Alastair Cook, to rebuild with a new set of values and goals," Flower said in a statement.
"This has been a very difficult decision to make and I remain committed to England cricket and would like to wish Alastair Cook and Paul Downton every success,” he said.
"I will remain in my position as a selector for the time being and am currently exploring possible roles within the ECB. The priority must now be to establish the direction and personnel needed to ensure England cricket moves forward," he added.
During his time in charge, the former Zimbabwe wicket-keeper batsman helped England to win the Ashes three times and masterminded their first World Twenty20 title in 2010.
Flower also steered England to number one in the world test rankings in August 2011 following a 4-0 home victory over India.
"Andy has been the most successful coach in England's history and we at the ECB are very disappointed to see him leave the role as Team Director," Paul Downton, managing director of England cricket, said.
"We respect his decision and the reasons for it but we are keen to keep Andy's experience and outstanding knowledge within the ECB,” he said.
"We are at advance stages of negotiating a role for Andy within the ECB structure which will best utilise his undoubted skills," he added.
The Zimbabwean, who had been in charge since 2009, found his position under increasing pressure after England suffered heavy defeats in the test series and he is now set to be given a new role with the national academy in Loughborough.