The USS John S McCain destroyer sailed within six nautical miles of Mischief Reef, part of the disputed Spratly Islands south of the Paracel Islands.
The Foreign Ministry pointed out that that the so-called USA "freedom of navigation" mission was carried out without authorization from Beijing, with has "indisputable sovereignty over the Nansha Islands (Spratley) and its surrounding waters".
China's foreign ministry said: "The US destroyer's actions have violated Chinese and worldwide laws, as well as severely harmed China's sovereignty and security".
"It is clear who is not willing to see stability in the South China Sea and who is the major factor pushing for militarization in the South China Sea".
U.S. Pacific Fleet spokeswoman Lt. Cmdr.
"All operations are conducted in accordance with worldwide law and demonstrate that the United States will fly, sail, and operate wherever global law allows", he said.
China has territorial disputes with its neighbours over the area.
An worldwide tribunal refuted China's claim to a large swathe of the South China Sea in 2016 in a case brought by the Philippines, though Beijing has rejected the ruling. "We told them we are a U.S. (ship) conducting routine operations in worldwide waters".
"That is true in the South China Sea as in other places around the globe", she said.
"The Spratly Islands consist of more than 100 small islands or reefs surrounded by rich fishing grounds - and potentially by gas and oil deposits", the CIA World Factbook said.
"The US provocation also forced the Chinese side to take measures to further enhance the national defense capability", it added.
Thursday's mission comes as the USA seeks greater Chinese involvement on resolving the tension over its neighbor, North Korea's, continuing missile tests, which are perceived in Washington as a serious threat to the United States and its regional allies.
Chinese authorities claim 90 percent of the area and have repeatedly said that the country's activities in the region are China's sovereign right.