Protests in Taipei had set back relations earlier this year - and Zhang Zhijun had to go around scores of anti-China demonstrators to enter a hotel for the talks - but he said he was very happy to be the first Taiwan Affairs Office minister to visit the island.
"To reach Taiwan from Beijing I flew three hours, but to take that step took no less than 65 years," he said in remarks opening the meeting with his counterpart Wang Yu-chi.
China has described the trip as a chance for Zhang to understand the island better. Analysts say he will likely keep a low profile as he travels around Taiwan through Saturday, avoiding strong political statements during scheduled chats with students, low-income people and a figure in Taiwan's anti-China chief opposition party.
China and Taiwan have been separately ruled since the Chinese civil war of the 1940s. China sees the island as part of its territory that eventually must be reunified - by force if necessary - despite a Taiwanese public largely wary of the notion of Chinese rule.
In 2008, Beijing set aside its military threats to sign agreements binding its economy to that of the investment-hungry island.
Dialogue opened that year as Taiwan President Ma Ying-jeou agreed to put off political issues to build trust and improve the island's economy through tie-ups with China's much larger one. The two sides have signed 21 deals, boosting two-way trade to $124.4 billion last year and bringing in about 3 million mainland tourists, who were once all but banned.
But in March, hundreds of student-led protesters forcibly occupied parliament in Taipei to try to stop ratification of a two-way service trade liberalization pact. The 24-day action dubbed the Sunflower Movement spiraled into the thousands, many of whom demanded an end to Taiwan's engagement with China, which they still see as an enemy.
On Wednesday Zhang compared China-Taiwan relations to taking a boat upstream.
"If it doesn't go forward, it goes backward," he said.
The two men discussed details of establishing first-ever consular-style offices to help to investors and tourists. They also agreed to renegotiate minor clauses of the services trade pact after it takes effect.
Despite the protests, Taiwan's parliament is expected to ratify the deal, although it's not clear when that would happen.
Taiwan says it will make no announcements during the visit, and the main opposition party says it will not organize protests against Zhang, though smaller protest groups are vowing to follow him. More than 100 scuffled with supporters at the airport and clashed with a column of police at the hotel, leaving one activist injured.
"Amid all these tensions this particular visit obviously is important in terms of trying to soothe sentiments and trying to stabilize relations," said Dali Yang, a China expert at the University of Chicago. "Any representative from the mainland, going to Taiwan, I think the best they can do is to try to stabilize relations."
But the lack of big protests doesn't mean that more Taiwanese want closer ties with China, analysts say.
"The best one could say is that a muting of protests would reflect a maturing of attitudes in Taiwan, and a greater willingness to listen and to express concerns in a less confrontational way," said Alan Romberg, East Asia Program director at The Stimson Centre, a Washington-based think tank. "But it would not mean that those concerns have disappeared."
Associated Press Writer Gillian Wong in Beijing contributed.