It is a dream come true for Morris, who has represented the county at all levels from under-11 upwards. "I have always wanted to captain the county, so I am delighted," he said.
Morris, 27, made his senior county debut in 2002 and was capped in 2008. He played for Durham University, where he was skipper for the last two of his three seasons, and British Universities, whom he also captained. He also appeared for the MCC.
Most of his club cricket has been with Falkland, though he did have short spells with Henley and Basingstoke & North Hants.
Berkshire chairman Cecil Fright said: "We are convinced James is the right man for the job. "It is an exciting time for Berkshire cricket with many young players coming into the team and we feel James is the best man to have in charge."
Finchampstead batsman Matt Jones, who returned to the county side last season, will be Berkshire's vice-captain for the 2013 season.