The demonstrators — some of them jobless after factory shutdowns and others independence activists and supporters of the opposition Democratic Progressive Party — vented their anger at President Ma Ying-jeou, who is also the Kuomintang chairman.
"Ma Ying-jeou, step down!" the crowd chanted while hurling shoes at riot police behind barricades.
A man was detained by police after climbing over barbed wire outside a gymnasium in the central city of Taichung, where the Kuomintang was meeting.
Pressure on Ma's administration has mounted after workers lost their jobs following the mass shifting of assembly lines from the island to the Chinese mainland to capitalise on cheap manpower and land prices there.
Inside the gymnasium, Ma urged party representatives to unify under the party's banner.
Only with the Kuomintang's continued rule could Taiwan "walk on the right path and thus give the people the most benefits", Ma said.
"But your support and unity is needed if we are to reach the goals." A row sparked by the expulsion from the Kuomintang of parliamentary speaker Wang Jin-pyng — the second most powerful politician in the party — had sparked fears the party would split.
Ma had accused Wang of influence-peddling and said he was unfit to head the legislature, but was overruled by a court ruling which allowed him to keep his post.
The party decided not to appeal the ruling, in the interests of unity. Wang was present at Sunday's congress.
Ma swept to victory in presidential polls in 2008 on a platform of strengthening trade and tourism links with former rival China. He was re-elected for a second and final four-year term in January 2012.
However, his approval ratings took a severe hit later that year after a bribery scandal implicating top cabinet official Lin Yi-shih, one of his key confidants.