According to an internal memo seen by Reuters, Thomas is relocating to New York to focus on Morgan Stanley's real estate business.
The Wall Street bank has yet to announce his successor.
Thomas' move is not a big surprise since he has been splitting his time between the Asian role and also as the chairman and CEO of Morgan Stanley's real estate investment.
Last week, Morgan Stanley made several changes to its top management in Asia, which resulted in Kate Richdale becoming the sole head of Asia Pacific investment banking business. The other co-head Gokul Laroia was made the head of equities for Asia, including Japan.
Finance Asia first reported Thomas's move.
A Morgan Stanley spokesman confirmed the content of the memo.
(Reporting by Denny Thomas; Editing by Ken Wills)