The People's Liberation Army (PLA) organised air and naval forces to warn the USS Preble to leave, said a PLA spokesman, after it entered waters near China-claimed Scarborough Shoal on Monday morning.
"The relevant actions from the US side endanger the safety of both Chinese and American ships and personnel, and undermine China's sovereignty and safety," said Li Huamin, spokesman of the PLA's Southern Theatre Command.
"We express our resolute opposition," he added.
The move comes as both countries adopt toughening stances on a host of economic and diplomatic issues, namely trade and hi-tech rivalry.
Earlier this month, US President Donald Trump hiked tariffs on $200 billion in Chinese goods, with China announcing it would raise tariffs on $60 billion in US merchandise from June 1 in retaliation.
Trump has also barred US companies from engaging in telecommunications trade with foreign companies said to threaten American national security.
Beijing has built artificial islands and military installations in the sea, including on the Spratly Islands, which Beijing calls Nansha.
China claims nearly all of the sea, though Taiwan, the Philippines, Brunei, Malaysia and Vietnam all claim parts of it.
The US Navy regularly conducts "freedom of navigation operations" to challenge Beijing's vast claims in the sea.
Earlier this month, two US warships entered waters adjacent to Gaven and Chigua reefs in the Spratlys, sparking fury from China.
"We strongly urge the US side to immediately stop such provocative actions so as to not harm China-US relations and the peace and stability of the region," said Chinese foreign ministry spokesman Lu Kang at a press briefing.