However, the Democratic Progressive Party [DPP], the opposition and organisers of the rally, is calling for a referendum on the pact, saying Taiwanese have a right to express their views before it is due to take effect.
The DPP said Taiwanese may gain short-term benefits from the tariff cuts, but that many local factories may be forced to shut down within a few years under an onslaught of cheap Chinese goods.
"The trade pact would turn Taiwan into another Chinese territory like Hong Kong,'' Chang Kuo-min, a rubber factory worker from central Changhua county, said.
"Taiwanese have worked so hard to achieve the democracy we have today, and we will not allow China to control us,'' he said.
Polls, however, indicate that more Taiwanese support the trade pact than oppose it.
The agreement was brought about by Ma Ying-jeou, Taiwan's president, as part of his policy of seeking closer economic ties with China in an effort to ease tension across the Taiwan Strait, a flash point since the two sides split amid civil war in 1949.
But some have suggested that closer political and economic ties could also serve China's long-term goal of returning the self-ruled island to its control, the fundamental aim of its Taiwan policy.
Taiwan said the deal will eventually create 260,000 jobs by attracting more Taiwanese and foreign investment on the island.
Under the pact, Taiwanese companies will receive tariff advantages on 539 products exported to China, while Chinese companies will receive advantages on 267 products in the Taiwan market.
Bilateral trade totals about $110bn a year, with $50bn in Taiwan's favour.
Since losing the presidency to Ma in 2008, the DPP has won six out of seven legislative by-elections and scored important gains in a series of local polls.
It hopes to use unhappiness over the the trade pact to achieve big gains in mayoral elections later this year and ultimately win the 2012 presidential election.
On Saturday, Ma said the trade agreement will be submitted to Taiwan's legislature for approval next month.
His ruling Nationalist Party holds a majority of the seats and the pact is expected to pass easily.