The USS John S McCain sailed within six nautical miles of Mischief Reef in the Spratly Islands on Thursday as part of a "freedom of navigation" operation, which prompted the Chinese navy to warn off the US destroyer.
Foreign ministry spokesman Geng Shuang said on Friday the operation had violated Chinese and international law, "seriously" impairing the country's sovereignty and security as well as "endangering lives".
"China is strongly dissatisfied with this," Geng said in a statement, adding Beijing would lodge an official protest with Washington.
Nicole Schwegman, spokeswoman for the US Pacific Fleet, said US military forces operate in the Asia Pacific region every day.
"All operations are conducted in accordance with international law and demonstrate that the United States will fly, sail, and operate wherever international law allows," she said.
Speaking on condition of anonymity, a US official told AFP news agency that a Chinese frigate sent radio warnings at least 10 times to the USS McCain.
"They called and said 'Please turn around, you are in our waters'," the official said. "We told them we are a US [ship] conducting routine operations in international waters."
The official said the interactions were all "safe and professional", with the operation lasting about six hours from start to finish.
Thursday's freedom of navigation operation was the third of its kind carried out by the US since President Donald Trump took office in January.
The operation comes four days after the US, Australia, and Japan denounced China's island-building and militarisation of the South China Sea on the sidelines of a security forum of the 10-nation Association of Southeast Asian Nations (ASEAN) in the Philippine capital, Manila.
China claims nearly all of the sea, through which $5 trillion in annual shipping trade passes and which is believed to sit atop vast oil and gas deposits.
However, in recent years, Beijing has managed to weaken regional resistance by courting some ASEAN members.
Chinese defence ministry spokesman Wu Qian said the situation in the South China Sea has "stabilised" because of "joint efforts" of China and neighbouring countries, but the US operation threatened "peace and stability in the region".
"The US military's provocative actions will only encourage the Chinese military to further strengthen the defence capacity building and firmly defend national sovereignty and security," said Wu.