The U.S. "freedom of navigation" operation has been previously conducted near China's reclaimed islands, called the Spratlys, or Nansha Islands, claimed also by the Philippines, Vietnam and Taiwan, among others.
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.
The head of China's air force has blasted a Japanese Defense Ministry white paper critical of Chinese military drills in and over waters near Japan, saying "the Sea of Japan is not Japan's sea".
Geng said the Chinese navy "identified the US warship, warned and expelled it".
In a statement in Beijing, Spokesperson of Chinese Foreign Ministry, Gen Shuang called upon the US administration to refrain from any further action detrimental to the China-US mutual trust and regional stability.
"China is very displeased with this and will bring up the issue with the United States side", the ministry added.
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 USA operation threatened "peace and stability in the region".
China, which claims the South China Sea virtually in entirety, has protested such repeated US military operations, which President Donald Trump's administration has continued partly to reassure allies locked in territorial rifts with Beijing.
At a time when China and South-East Asian countries have agreed to solve and manage the South China Sea issue through bilateral talks and to avoid influence by non-regional forces, the USA behaviour shows that Washington wants to maintain its presence in the region, instead of solving the issue, Zhou said.
An global 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. China has ignored and dismissed the ruling as a sham.
China had the largest volume of exports passing through the disputed territory, or $US874 billion, and therefore the most to lose if commercial trade routes were disrupted by conflict. It also gives states an exclusive economic zone up to 200 nautical miles from their coastline meaning that most of the Spratly Islands are in the territorial waters of the Philippines and Malaysia.
But Beijing's reaction to the latest American naval operation has underscored that China has its own geopolitical sore points with the White House, including weapons sales to Taiwan and the repeated freedom of navigation operations in the South China Sea.
Zhang from Lingnan University said there could be more pressure applied by other rivals such as the US, Australia and Japan, which have previously voiced opposition to land reclamation and militarisation in the disputed waters, upsetting Beijing.