Beijing accused the U.S. of entering Chinese waters without permission and engaging in provocations that threaten China's sovereignty.
Monday's operation was carried out "to challenge excessive maritime claims and preserve access to the waterways as governed by global law", Commander Clay Doss, a spokesman for the US Navy's 7th Fleet, said. "China urges the United States to immediately stop such provocative actions and earnestly respect the efforts by regional countries to maintain the peace and stability of the South China Sea".
Soybeans closed lower on Monday while grains were little changed amid pessimism about the ongoing trade talks between the US and China.
The US and its allies periodically send planes and warships near South China Sea islands and reefs claimed by Beijing to signal their right under worldwide law to pass through the waters, invariably angering China.
The US is "determined to stir up trouble in the South China Sea, create tension and undermine peace", Hua said.
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters, where Chinese, Japanese and some South-east Asian navies operate.
During a South China Sea freedom-of-navigation operation in September, a Chinese destroyer challenged a US vessel to a showdown, forcing the US Navy ship off course and risking a deadly collision.
The rising military tension comes against the backdrop of an increasingly bitter trade war between China and the US.
China claims a large part of the South China Sea, and has built artificial islands and air bases there, prompting concern around the region and in Washington. "That is true in the South China Sea as in other places around the globe", he said.
Top US officials have attacked China for everything from human rights abuses to cyber espionage in America.
China says the construction is necessary for defence, and it was the United States that was responsible for tensions by sending warships and military planes close to islands Beijing claims.
Other regional nations-such as the Philippines and Vietnam-lay claim to part of the waterway and the US routinely pushes back against China by sending ships to patrol the sea.
The two countries are also at odds over regional security, including Washington's overtures to the self-ruled island of Taiwan, which China claims as its own.