Sanctions will apply to NGOs that had acted "badly" over the recent unrest in Hong Kong, China's foreign ministry spokeswoman Hua Chunying said, including the National Endowment for Democracy, Human Rights Watch and Freedom House.
China suspended US warship visits and sanctioned American NGOs on Monday in retaliation for the passage of a bill backing anti-Beijing protesters in Hong Kong.
The semi-autonomous financial hub has been rocked by nearly six months of increasingly violent unrest demanding democracy, which Beijing has frequently blamed on foreign influence.
Last week, US President Donald Trump signed the Hong Kong Human Rights and Democracy Act, which requires the president to annually review the city's favourable trade status and threatens to revoke it if the semi-autonomous territory's freedoms are quashed.
The move came as the world's two biggest economies have been striving to finalise a "phase one" deal in their protracted trade war.
"In response to the unreasonable behaviour of the US side, the Chinese government has decided to suspend reviewing the applications for US warships to go to Hong Kong for (rest and) recuperation as of today," foreign ministry spokeswoman Hua Chunying said at a regular press briefing.
China had already denied requests for two US Navy ships to dock in Hong Kong in August, without specifying a reason why.
Hua said they would also apply sanctions to a number of US-based NGOs, although failed to give any specifics over the form sanctions would take.
Sanctions will apply to NGOs that had acted "badly" over the recent unrest in Hong Kong, she said, including the National Endowment for Democracy, Human Rights Watch and Freedom House.
There was "already a large amount of facts and evidence that make it clear that these non-governmental organisations support anti-China" forces and "incite separatist activities for Hong Kong independence", Hua added.
She accused them of having "great responsibility for the chaotic situation in Hong Kong".
Protesters in Hong Kong are pushing for greater autonomy and police accountability, but the city's pro-Beijing leadership has refused any major political concessions.
The increasingly violent rallies have hammered the retail and tourism sectors, with mainland Chinese visitors abandoning the city in droves.
The city's finance chief warned Monday that Hong Kong is set to record its first budget deficit in 15 years.