"My understanding is that they will sign it," the Florida senator said on "Squawk Box."
The House on Wednesday evening passed the measure, which already received unanimous Senate approval, by a 471-1 margin. Rep. Thomas Massie, R-Ky., was the lone dissenter. Formally called the Hong Kong Human Rights and Democracy Act, the bill aims to protect anti-government protesters in Hong Kong from heavy-handed Chinese interference. It's now up to Trump on whether to sign it into law.
The measure, co-sponsored by dozens of bipartisan lawmakers including Rubio, mandates sanctions on Chinese and Hong Kong officials who carry out human rights abuses and requires an annual review of the favorable trade status that Washington grants Hong Kong, a semi-autonomous territory of China.
Hong Kong held on to its advantageous trading status with the U.S., even after the handover from British to Chinese rule in 1997, in recognition of Beijing's pledge to allow Hong Kong to retain its own laws, judiciary and freedoms. In recent months since the demonstrations started, there's been growing concern that China might go back on its promise and exert power over Hong Kong.
Chinese Foreign Ministry spokesman Geng Shuang said Beijing "condemns and firmly opposes" the human rights bill, which comes at a time of economic and trade tensions between the U.S. and China.
Rubio said those conflicts between the world's two biggest economic powers won't be resolved quickly.
"I think it's going to take more than one presidency," said Rubio, who unsuccessfully sought the 2016 GOP presidential nomination. He called the negotiations a 10-year to 15-year "balancing act."
Beijing and Washington have remained locked in an escalating trade war for well over a year, with each side placing tariffs on billions of dollars' of each others' goods. Trump announced last month that Beijing agreed to an initial trade deal that would address intellectual property and financial services concerns, as well as Chinese purchases of about $40 billion to $50 billion in U.S. agricultural products.
Chinese Vice Premier Liu He, according to The Wall Street Journal, has invited U.S. Trade Representative Robert Lighthizer and Treasury Secretary Steven Mnuchin to Beijing for a face-to-face talks on a "phase one" trade deal.
Even if that first-step trade deal, which some call a "skinny deal," is reached, it won't touch on all of the issues between the two nations, Rubio said. "We still have to stop thinking about our conflict with China as one issue.
"There isn't one deal that's going to deal with all of these things," the senator said, adding "it's not the same as USMCA," the United States-Mexico-Canada Agreement. "It's a much broader geopolitical balance."
Rubio's been tough on China's alleged interference in the United States. In September, he called on the government to ensure that federal worker retirement dollars are not being invested in China.
"There really is no such thing as private companies in China," the senator said at the time. "They're all, to some extent, instruments of state power."
— The Associated Press contributed to this report.