Mr Chen is in Taiwan to sign a series of trade deals
Demonstrators have dispersed after surrounding a hotel in the Taiwanese capital to protest against a visit by a top-ranking Chinese negotiator.
Hundreds of protesters gathered at the hotel in Taipei where Chinese envoy Chen Yunlin was attending a dinner.
Mr Chen is reported to have left the hotel after a six-hour stand-off between demonstrators and police.
The demonstrators are opposed to President Ma Ying-jeou's policy of forging closer ties with China.
The BBC's Cindy Sui, who is at the scene, says vehicles with tinted windows leaving the hotel were spat and yelled at.
Some shouted "Ma Ying-jeou step down", blaming the Taiwanese president for allowing the landmark talks during Mr Chen's visit.
Lines of riot police prevented demonstrators from getting into the hotel.
Mr Chen is the most senior Chinese official to visit Taiwan in decades.
The envoy is spending five days in Taiwan and has already signed agreements to improve direct trade and transport links between the two sides.
He is due to meet President Ma on Thursday.
Mass protests against President Ma's pro-China policies have been on going since August.
They have been led by the main opposition, the Democratic Progressive Party (DPP), which while in government antagonised Beijing with a pro-independence agenda.
Recent relations soured two months ago when Taiwan was affected by tainted milk products from China, and a number of people were taken ill.
China claims sovereignty over Taiwan though they have been separately governed since 1949.