But Siew's Nationalist Party, which won elections last month, favours eventual unification with China, although Ma Ying-jeou, the president-elect, has placed the issue on the back burner.
The regional conference is seen as the first major test of the incoming Ma administration's ability to bring about better ties with China.
Hu said that the talks were an opportunity to work towards economic co-operation between China and Taiwan.
"The current cross-Strait economic exchange and co-operation are faced with an important historical moment which requires both sides to work together," he said.
Siew told Hu that he was "an old hand" on economic issues, as the two leaders met.
"I hope we can strengthen economic co-operation," he said.
Andrew Yang, the secretary-general of The Chinese Council of Advanced Policy Studies, an independent think-tank, told Al Jazeera that the meeting would work as a trust building exercise between the two nations.
"I think this is a symbolic meeting between the two senior leaders from both the sides, because they are willing to set aside disputes and talk to each other. I think that will establish a good communication between the two sides," he said.
Ma, the more China-friendly of two candidates in last month's election in Taiwan, has vowed to improve relations with the mainland, increase trade, tourism and transport links, and work on a peace treaty to end hostilities.
China has become Taiwan's number one export market and its biggest trading partner.
Two-way trade last year reached a record $102bn. The US has welcomed the meeting, describing it as the "best way forward".
"We think that dialogue between the People's Republic of China and the authorities, leaders on Taiwan is the best way forward," John Negroponte, the US deputy secretary of state, in Washington, said.
China hopes the Boao Forum will become the regional version of the Davos meetings.