The Charles de Gaulle docked on Friday at Subic Bay, a former US Naval base northwest of Manila, for a break after more than two months of deployment in the Indo-Pacific.
The French carrier engaged with security allies for contingency readiness and to promote regional security, including with Filipino forces, navy ships and fighter jets.
They held anti-submarine warfare drills and aerial combat training on Friday in the South China Sea, Philippine and French officials said.
Last year, the French navy deployed a frigate for the first time to participate in a joint sail with US and Philippine counterpart forces in and near the disputed waters.
It was part of the largest annual combat exercises in years by US and Filipino allied forces, involving more than 16,000 military personnel.
China strongly criticised the exercises then, saying the Philippines was "ganging up" with countries from outside Asia in an obvious reference to the US and its security partners, and warned the drills could instigate confrontation and undermine regional stability.
The Charles de Gaulle, the only nuclear-powered aircraft carrier in the world other than those of the US Navy, led a strike group that included three destroyer warships and an oil replenishment ship in its first-ever visit to the Philippines, French officials said.
France has been shoring up its military engagements with the Philippines and other Southeast Asian nations at odds with China in the disputed waters, a key global trade and security route although it says those emergency-preparedness actions were not aimed at any particular country.
China, however, has bristled at any presence of foreign forces, especially the US military and its allies, which carry out war drills or patrols in the South China Sea, which Beijing claims almost in its entirety although it has not publicly released exact co-ordinates of its claim other than 10 dashed lines to demarcate vaguely what it calls its territory on maps.
Two weeks ago, Australia protested after a Chinese J-16 fighter jet released flares that passed within 30 metres of an Australian P-8 Poseidon surveillance jet over the South China Sea.
The Australian military plane did not sustain any damage and no crew member was injured in the February 11 incident.
A Chinese Foreign Ministry spokesperson accused the Australian aircraft of "deliberately" intruding into airspace over the disputed Paracel Islands, which China and Vietnam contest.
France and the Philippines began talks last year on a defence pact that would allow troops from each country to hold exercises in the other's territory.
The Philippines has also signed such status-of-forces agreements with the US and Australia.
