Since the defeated Republic of China government fled to Taiwan in 1949 after losing a civil war to Mao Zedong's communists, no serving Taiwanese leader has visited China.
Ma, president from 2008 to 2016, in 2023 became the first former Taiwanese leader to visit China, and is on his second trip to the country, at a time of simmering military tension across the strait.
Ma had been widely expected to meet Xi this time around, having first met Xi in Singapore in late 2015 for a landmark summit shortly before the current Taiwan president, Tsai Ing-wen, won election.
Meeting Ma on Wednesday in Beijing's Great Hall of the People, where foreign leaders normally hold talks with top Chinese officials, Xi said that people on both sides of the strait are Chinese.
"External interference cannot stop the historical trend of reunion of the country and family," Xi said, in comments reported by Taiwanese media.
Xi did not elaborate but in Chinese terminology referring to external interference over Taiwan is generally aimed at the support Taipei gets from Western countries such as the United States, especially arms sales which infuriate Beijing.
People on both sides of the strait were Chinese, Xi said.
"There is no rancour that cannot be resolved, no problem that cannot be discussed, and no force that can separate us."
China has never renounced the use of force to bring democratically-governed Taiwan under its control, and has ramped up military and political pressure to assert its sovereignty claims.
Ma told Xi that tensions had caused unease for many Taiwanese.
"If there is a war between the two sides, it will be unbearable for the Chinese people," Ma said, using a term that refers to people who are ethnically Chinese rather than their nationality.
"Chinese on both sides of the strait absolutely have enough wisdom to handle all disputes peacefully and avoid heading into conflict."
Tsai and her government reject China's territorial claims, saying only the island's people could decide their future.
China says it will only talk to Tsai if she accepts that both sides of the strait are part of "one China", which she has refused to do.
Xi has only rarely made public remarks about Taiwan in recent months.
Speaking to US President Joe Biden in early April, Xi urged Washington to translate "Biden's commitment of not supporting 'Taiwan independence'" into concrete actions.
