Zhang Yaqin was a vice president and led Microsoft's Asia-Pacific research department.
"Zhang Yaqin will start as president for new business on September10," a Baidu spokesman said.
Microsoft has been under pressure from the government for months.
Investigators have begun anti-trust proceedings against the company, and there is a ban on installing the Windows 8 operating system on official computers.
Microsoft has been struggling to generate more revenue from the use of its operating system in China, where it holds a dominant position, but only due to the large number of pirated copies.
A state-backed alliance of developers is planning to release a Chinese operating system later this year.
DPA