The visit came as China said one of its highest-ranking military officials had also visited the region recently.
Tensions have escalated in the South China Sea in recent years, with China steadily expanding its military presence in the region.
This week the US and the Philippines agreed to conduct joint patrols there.
China claims most of the sea as its own and has become increasingly assertive.
Ash Carter arrived on board the USS John C Stennis on Friday and gave a statement alongside Philippine Defense Secretary Voltaire Gazmin.
"What's new is not an American carrier in this region," he said. "What's new is the context of tension which exists, which we want to reduce."
He said that the US wanted to work together with China and that the trip was meant to show support for allies, rather than provoke Beijing.
The US has expanded its support for allies in the South Pacific in recent months, following China's military build-up - which includes the construction of islands with airstrips.
China, which claims a wide swathe of the sea, has been reclaiming land around reefs.
The US and other countries have called for the halt of such activities, accusing China of militarisation but Beijing has insisted that the construction is for civilian purposes.
Last week, US military officials announced they would send $40m (Â£28m) in military assistance to the Philippines to increase intelligence-sharing, surveillance and naval patrols.
Contested South China Sea
The US Defence Secretary, Ash Carter, has visited an American aircraft carrier in the contested waters of the South China Sea.