The decision by Zhao Jing is believed to be part of management restructuring by the investment bank, according to the Wall Street Journal.
Ms Zhao has worked for Morgan Stanley since 1994 and was the company's chief representative in Beijing. She played a lead role in the 2005 $9.2 billion initial public offering (IPO) of China Construction Bank Corp.
According to reports, Ms Zhao is considering a move to rival bank Citigroup. Her decision to leave follows a recent spate of resignations in Morgan Stanley's Asian operations.
The head of Morgan Stanley's Chinese operations, Jonathan Zhu, resigned in January this year after 11 years with the bank to take up a post at US equity company Bain Capital.
Wei Christianson, former head of China investment banking at rival Citigroup, will take over from Mr Zhu in May.