HRW said the move to block Kenneth Roth highlighted "vanishing freedoms" as a result of pressure from Beijing. Hong Kong has been gripped by months of anti-government protests.
China had threatened sanctions on HRW and other American NGOs, which it said supported "anti-China" forces. In a video filmed at Hong Kong International Airport and shared on Twitter, Mr Roth - a US citizen - said officials told him he was barred for "immigration reasons", even though he had visited the city before. The BBC has contacted Hong Kong's immigration department for comment.
This year's HRW annual World Report, Mr Roth said, focused on "how the Chinese government is trying to deliberately undermine the international human rights system, not simply to suppress the rights of people at home but also undermine the ability of anybody else to try to hold China to human rights standards".