The pilot managed to eject the plane before hitting the deck.
7th Fleet spokesman Lieutenant Mark Langford told the Associated Press that the pilot had been recovered from the helicopter.
Seven sailors were injured and three were taken to a hospital in Manila, Philippines, for treatment. They are in stable condition.
Meanwhile, four people on the ship were treated and three were released, according to the US Pacific Fleet.
Langford revealed that the damage to the deck was "superficial" and that regular flying practice has resumed.
It is not known why the incident happened as the investigation is on and details about the accident are still being verified.
USS Carl Vinson is practicing in the South China Sea with the USS Abraham Lincoln.
More than 14,000 sailors and sailors are participating in the exercise.
The US often practices "freedom of navigation" operations in the South China Sea, which is in line with international law.
The military says the aim of the exercise is to "deliver the powerful maritime force of the US Indo-Pacific Command Joint Force".
With China increasing its pressure on Taiwan, the US and its allies have intensified their exercises in the South China Sea region.
Regular practice
China has often regarded Taiwan as a "renegade" state and has repeatedly vowed to take it back by force if necessary.
Taiwan broke away from China in a civil war in 1949, but Beijing considers the island its territory.
It is believed that a formal declaration of independence would be a potential trigger for a possible conflict as Washington tries to prevent Beijing from seizing the island by force.
According to Taiwan's Defense Ministry, China has flown 39 warplanes towards Taiwan in its latest offensive to claim power in the region.
This included 24 J-16 fighter jets, 10 J-10 jets, a nuclear-capable H-6 bomber and other support aircraft. They were engaged in anti-submarine air and combat readiness exercises.
Beijing declined to give details of why they flew the plane but said it was not a "diplomatic matter".
Taiwan's military issued radio warnings and deployed air defense missiles to monitor movements.
Colin Koh, a research fellow in Singapore, told CNN: "There is no doubt that this is part of a broader campaign by Beijing aimed at eroding Taiwan's willingness and ability to continue with resistance."
Projecting power
The US Navy's nuclear-armed submarine was sighted for the first time in decades amid rising tensions with Beijing.
The top-secret USS Nevada, which was pictured at a Guam naval base, is known as "Boomer" and is armed with 20 Trident nuclear missiles.
Thomas Shugart, a former US Navy submarine captain and now an analyst at a new US security center, said Nevada's presence sends a "message".
He told CNN: "We can park about 100 nuclear weapons at your door and you won't even know about it or you won't be able to do much about it."
It is extremely rare for such ships to be photographed outside their home ports of Bangor, Washington and Kings Bay, Georgia.
Earlier this month, President Xi urged countries to move away from a "cold war mentality".
Speaking at the Davos Agenda virtual event, he said: “We need to abandon the Cold War mentality and look for peaceful coexistence and the results of victory.
"Acts of prevention, suppression, or conflict arising therefrom all cause harm, not the least good, to world peace and security.
“History has proved time and again that confrontation does not solve problems. It only invites disastrous consequences."