"Although the Chinese mainland and Taiwan have been separated since 1949, the fact that the two sides belong to one China has not changed, and will not be changed," he said.
Reunification will end political confrontation but it does not mean remoulding territory and sovereignty, Xi told a visiting Taiwanese delegation of pro-reunification groups.
The basic guideline to solve the Taiwan question is "peaceful reunification; one country, two systems" and it is also the best way to realise national reunification, he was quoted as saying by state-run Xinhua news agency.
Hong Kong, a former British colony was reunited with China in 1997 under the "One country, Two systems" formula under which the "special administrative region" was granted a degree of autonomy.
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Xi, who is also the General Secretary of the ruling Communist Party of China (CPC) vowed to take "a firm and unwavering stance" on national reunification.
"We treat our Taiwan compatriots equally and without discrimination. We welcome anyone willing to promote peaceful cross-Strait development, whatever stance he once took," he said.
Curbing secessionism is a must for ensuring the peaceful development of cross-Strait ties, he said in a rare strongly worded message from top Chinese leader in the midst of efforts to bring about rapprochement with sustained dialogue.
"Secessionists have harmed national sovereignty, territorial integrity and cross-Strait peace and stability," Xi said.
He warned that secessionists would not give up easily and would continue to provoke cross-Strait enmity and hinder exchange and cooperation.
"One country, Two systems" in Taiwan will take the island's actual condition into consideration, absorb suggestions from both sides and fully consider the interests of Taiwan compatriots, Xi added.
Under the formula there would be only one China, but distinct regions like Hong Kong and Macau are allowed to maintain their own politico-economic systems.