The events on and around the central Beijing square on June 4, 1989, when Chinese troops opened fire to end student-led pro-democracy protests, are not publicly discussed in China and the anniversary is not officially marked.
Rubio said on Wednesday that Beijing's censorship could not erase memories of the military assault.
"Those who sacrificed to uphold their unalienable rights of free expression and peaceful assembly will be vindicated some day," he said in a statement that followed past practice of the United States' top diplomat marking the anniversary.
Speaking in Beijing, Chinese foreign ministry spokeswoman Mao Ning said the government had long reached "a clear conclusion" about the "political turmoil that occurred in the late 1980s", reiterating Beijing's stance.
"China is strongly dissatisfied and firmly opposed to the US distorting historical facts, smearing China's political system and development path," Mao said of Rubio's statement on Thursday.
She also accused the US of interfering in China's internal affairs "on the pretext of" democracy and human rights, and defended Beijing's "path of socialism with Chinese characteristics".
Public commemorations of the crackdown take place in overseas cities, including Taipei, where senior Taiwanese government leaders often use the anniversary to criticise China, which views democratically governed Taiwan as its own territory.
Writing on his Facebook page, Taiwan President Lai Ching-te said a truly great country should not "blindly believe in military might or engage in militarism".
"I sincerely hope that China can face up to the June 4 incident of 37 years ago, acknowledge the truth, soothe the pain, and open the door to reconciliation and dialogue," he said.
China's Taiwan Affairs Office did not respond to a request seeking comment on Lai's remarks.
Chinese tanks rolled into Tiananmen Square before dawn on June 4, 1989, crushing weeks of pro-democracy demonstrations by students and workers.
China has never provided a full death toll, but rights groups and witnesses say the figure could run into thousands.
China blamed the protests on counter-revolutionaries seeking to overthrow the ruling Communist Party.
In Hong Kong, where a candlelight vigil in the city's Victoria Park once drew tens of thousands of people each year, public remembrances came to an end after Beijing imposed a national security law in 2020.
Several vigils were still expected to take place in a number of cities around the world on Thursday, including four in Germany and one in Australia.
