Lien Chan, also an honorary chairman of Taiwan's ruling Kuomintang (KMT) party, met President Xi Jinping at the Diaoyutai State Guesthouse in Beijing, the official Xinhua news agency said. It did not immediately provide details of what was discussed.
The four-day visit by Lien, who arrived on Monday, follows the first government-to-government talks between Taiwan and China since they split 65 years ago after a civil war.
In an apparent nod to the political sensitivities of China-Taiwan encounters, the Xinhua report described Xi by his party title of "general secretary of the Communist Party of China Central Committee" rather than as state president.
According to Taiwan's Central News Agency, Lien told reporters in Taipei Monday that he was not representing any organisation or political party, nor would he convey any message to Xi from Taiwan President Ma Ying-jeou.
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Exactly a week ago, Wang Yu-chi, Taiwan's top official overseeing China policy, met his Chinese counterpart Zhang Zhijun in Nanjing, in a symbolic yet historic move between the former bitter rivals.
Beijing still claims the self-ruled island as part of its territory awaiting reunification.
Lien became the first leader of the KMT, or Nationalist, party to visit China in 56 years when he met President Hu Jintao in 2005 to formally end hostilities with the Communists. Last year, Lien met Xi in Beijing.