Wednesday's protest against Chen Yunlin comes a day before the expected signing of a deal that may further encourage investment on both sides of the Taiwan Strait.
Taiwanese businesspeople on the mainland see it as particularly important in safeguarding their interests. They have already invested more than $120 billion in China.
The pro-independence Taiwan Solidarity Union led the anti-Chen protests. The TSU says China is using the lure of economic benefits to further its goal of bringing Taiwan under its control.
China and Taiwan split amid civil war in 1949. Traditionally tense bilateral relations have improved considerably since Taiwanese President Ma Ying-jeou took office in 2008.