Clinton urged China to openly look into the June 3-4, 1989, incident and give an accounting of those killed, missing or detained during the military crackdown.
Without making a direct reference to Tiananmen Square, Chinese Foreign Ministry spokesman Qin Gang said his country expressed deep dissatisfaction and resolute opposition to her remarks, Xinhua reported.
"As to the political turmoil and problems that happened in the late 1980s, the Communist Party of China and the Chinese government have already made a clear conclusion," Qin said.
He said facts had proven the path of socialism with Chinese characteristics suited the national conditions of China and complied with the fundamental interests of the overwhelming majority of the Chinese people, the state-run news agency said.
The Chinese Communist Party refers to the 1989 uprising as counter-revolutionary.
Clinton's statement said the 20th anniversary "provides an opportunity for Chinese authorities to release from prison all those still serving sentences," and urged China to give the same importance to protecting human rights and democratic development as it does its economic reform.
Qin said the remarks disregarded facts and made random accusations against the Chinese government.
"We urge the United States to put aside its political prejudices and correct its wrong-doings so as to avoid interfering with and damaging Sino-U.S. relations," Qin said.