The strike group travelled into the Taiwan Strait on Thursday led by the USS Ronald Reagan. Training included flight operations with fixed and rotary-wing aircraft.
The group also undertook maritime strike exercises and coordinated tactical training, the US Navy said in a statement.
The US regularly sends warships through the disputed waterway, an action which China condemns.
China claims nine-tenths of the South China Sea, through which some $4trillion (£3.06trillion) of trade passes each year.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam also have competing claims.
The US Navy said the exercise was done to “build and maintain war fighting readiness that is responsible, flexible, and honours enduring commitments to mutual defence agreements with regional allies and partners”.
The navy stressed the operations were “lawful” with strike group commander Rear Adm. George Wikoff, adding: “Throughout our deployment, we continue our long tradition demonstrating the United States’ commitment to the lawful use of the seas and maintaining open access to the international commons.”
Prior to arriving in the South China Sea, the USS Reagan was operating in the Indian Ocean before returning through the strait.
However, China said the United States was seriously undermining peace and stability in the Taiwan Strait over their military exercises and deployments.
The White House is pushing forward to sell Taiwan sophisticated military equipment including MQ-9 drones and a coastal defence missile system fuelling further tensions.
China and the United States have also recently been at loggerheads over a range of other issues from the coronavirus pandemic to trade and human rights.