Democratically ruled Taiwan has come under increased military and political pressure from Beijing to accept its sovereignty, but Taipei has pledged to defend their freedom and that only Taiwan's people can decide their future.
Speaking at Beijing's Great Hall of the People, Xi said the Chinese people have a "glorious tradition" of opposing separatism.
"Taiwan independence separatism is the biggest obstacle to achieving the reunification of the motherland, and the most serious hidden danger to national rejuvenation," he said on the anniversary of the revolution that overthrew the last imperial dynasty in 1911.
"The historical task of the complete reunification of the motherland must be fulfilled, and will definitely be fulfilled."
China's air force mounted four straight days of incursions into Taiwan's air defence zone from Oct 1, involving close to 150 aircraft, though those missions have since ended.
Taiwan says it is an independent country called the Republic of China, its formal name.