Shouting slogans like "Defend Taiwan's sovereignty", "We reject United Front" and "Communist rebels go home", members of the Taiwan Solidarity Union clashed with the police as the delegation from Shanghai arrived, Efe news reported.
One protestor, dashing towards the Chinese contingent holding anti-Chinese leaflets, was pinned down to the ground and taken away by police.
The protest took aim at the delegation leader Sha Hailin, a Communist Party official and head of Shanghai's United Front Work Department which promotes Taiwan-China unification.
However, several pro-China groups welcomed the Chinese by shouting slogans and holding up placards.
The delegation will on Tuesday attend the annual Taipei-Shanghai Forum, nicknamed the twin-city dialogue, and will sign three agreements on cultural and sports exchange.
The forum is one of the few exchanges Beijing has allowed to exist despite worsening ties since President Tsai Ing-wen took office on May 20.
Beijing threatened to isolate Taipei through trade and diplomatic means after Tsai refused to accept the one-China policy that claims Taiwan as a part of China.
China considers Taiwan as a breakaway Chinese province awaiting reunification with the mainland.
But Taiwan claims it is a sovereign country, currently recognised by 22 countries.
