The highly symbolic visit comes amid an increasingly tense political climate.
Official celebrations are planned, as well as large protests from pro-democracy and pro-Beijing camps.
Several well-known activists were arrested on the eve of Xi Jinping’s arrival.
The group, which included student leader Joshua Wong, had staged a protest at an iconic sculpture symbolizing the handover.
The golden sculpture of a bauhinia flower – Hong Kong’s emblem – by the city’s harbor was a gift from China.
President Xi Jinping arrived for the three-day visit with his wife Peng Liyuan at Hong Kong’s main Chek Lap Kok airport. The couple was welcomed by a marching band and children waving flags.
In a brief speech on the tarmac, President Xi said Hong Kong was “always in my heart”.
Beijing’s central government “has always been a strong backer of Hong Kong” and “will, as always, support Hong Kong’s economic development and improvement of people’s lives”.
President Xi also said Beijing was “willing to work with all sectors of Hong Kong’s society in maintaining Hong Kong’s extraordinary journey these past 20 years”, and would “ensure ‘one country, two systems’ will continue with stability”.
Hong Kong was handed back from British to Chinese rule in 1997.
Beijing agreed to govern it under “one country, two systems”, granting the city its own legal system, limited democracy with multiple political parties, and rights like freedom of assembly and free speech.
However, China’s growing influence has been met with unease and concerns that the mainland could undermine Hong Kong’s more politically liberal traditions.
Activists have been campaigning for years for Hong Kong to have more political freedom.
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