Foreign ministry spokesman Geng Shuang said on Friday the operation had violated Chinese and global law, "seriously" impairing the country's sovereignty and security as well as "endangering lives".
Beijing says US Navy warship sailing near disputed region violated worldwide law and threatened its sovereignty. China has used dredged sand to expand the original reef into an artificial island big enough to hold an airstrip.
The United States does not recognize China's claim of sovereignty in that location and regards the area as global waters.
"Some external forces wish to go against the tide and provoke troubles in the name of "freedom of navigation", aiming to destroy the good atmosphere".
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.
It's true in the South China Sea.
In addition to freedom-of-navigation operations, the US has also conducted bomber overflights in the South China Sea.
Major construction at three of China's large man-made islands in the Spratly's has wrapped up, according to a separate AMTI report from March, allowing Beijing to deploy fighter jets and mobile missile launchers to the area at any time. Neither China's defence ministry nor its foreign ministry immediately responded to a request for comment from Reuters.
The Trump administration did manage to get China and Russia's support for a unanimous 15-0 UN Security Council resolution last weekend which aimed to take a billion dollars in exports away from the rogue communist regime.
"China is very displeased with this and will bring up the issue with the USA side", the ministry said in a statement.
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters, and comes as Trump is seeking China's cooperation to rein in North Korea.
Geng said, "China has the firm determination to safeguard its territorial sovereignty and maritime interests".
AMTI made Tree Island and North Island as examples.
"We told them we are a U.S. ship conducting routine operations in worldwide waters".
"All operations are conducted in accordance with global law and demonstrate that the United States will fly, sail, and operate wherever worldwide law allows", he said.
The U.S. Defense Department says FONOPs represent "a challenge to excessive maritime claims".
The US move came four days after the United States, Australia and Japan denounced Beijing's island-building and militarization of the South China Sea on the sidelines of a security forum of the 10-nation Association of Southeast Asian Nations (ASEAN) in Manila.
The archipelago is claimed in its entirety by China, Taiwan and Vietnam, while portions are claimed by Malaysia and the Philippines.