"The US destroyer's actions have violated Chinese and global laws, as well as severely harmed China's sovereignty and security", Chinese Foreign Ministry Spokesperson Geng Shuang said in a statement.
"China holds indisputable sovereignty over Nansha Islands and surrounding waters", Beijing's defense ministry said.
AMTI said China continued to reclaim in the Paracel Islands. Sailing within those 12 miles is meant to show that the United States does not recognize territorial claims there.
"However, some parties from outside continue to meddle in the region under the guise of free navigation", Geng said.
In July, a US warship sailed near a disputed island in the South China Sea claimed by China, Taiwan, Vietnam.
China claims almost 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.
Thursday's operation came as U.S. President Donald Trump seeks Chinese cooperation in reining in North Korea's missile and nuclear programs, and could complicate efforts to work together toward that end.
The U.S.is reportedly concerned that China's construction of artificial islands and build-up of military facilities in the South China Sea are meant to restrict nautical movement in the area.
Experts and officials have criticized former President Barack Obama for potentially reinforcing China's claims by sticking to innocent passage, in which a warship effectively recognized a territorial sea by crossing it speedily without stopping.
Washington welcomed the joint communique issued by the foreign ministers of the Association of Southeast Asian Nations addressing the South China Sea issue.
Geng reiterated the Chinese government's willingness to safeguard national sovereignty and its maritime rights and interests. "All operations are conducted in accordance with worldwide law and demonstrate that the United States will fly, sail, and operate wherever global law allows".
On Thursday, State Department spokeswoman Heather Nauert was asked at a briefing whether "freedom of navigation" and other issues serve to "make for a more hard campaign on North Korea with China".
"They called and said "please turn around, you are in our waters", the official said.
"We told them we are a usa ship conducting routine operations in worldwide waters".
Earlier in the week, Wang said talks on a nonaggression pact aimed at preventing clashes from erupting in the South China Sea may start this year if "outside parties" don't cause a major disruption, in an apparent reference to Washington and allies such as Japan.
Foreign Affairs Secretary Alan Peter Cayetano, chair of this year's Asean foreign ministers meetings, admitted that he did not want land reclamation and militarization in the South China Sea to be mentioned in the joint communiqué.