In the meeting with General Fan Changlong, a deputy head of China's powerful Central Military Commission, Carter stressed his commitment to developing "a sustained and substantive US-China military-to-military relationship", the Pentagon said.
It said this would be based on a shared desire to deepen cooperation in areas including humanitarian assistance, disaster response, peacekeeping, counter-piracy, as well as "constructive management of differences".
In reiterating US concerns about tensions in the South China Sea, Carter called on China and all rival claimants to halt land reclamation and militarization of disputed territory, and to pursue a peaceful resolution in accordance with international law, the Pentagon statement said.
Carter also reaffirmed his commitment to reach a consensus by September on a memorandum of understanding aimed at reducing the risk of accidents when the two countries aircraft operate in close proximity, the statement said.
Fan told Carter that China's construction work in the South China Sea was mostly to improve living conditions in order to better protect its sovereignty. He also said China had a right to build on its own territory and deploy forces there, China's Defence Ministry said.
Fan also urged the United States to stop its military activities in the South China Sea.
"The South China Sea issue is only an interlude in Sino-US ties and both sides should look further ahead and pay attention to more important and bigger international and regional issues," it paraphrased Fan as saying.
Fan's visit to the Pentagon was part of a week-long trip to the United States, which will include a meeting with US National Security Adviser Susan Rice at the White House on Friday. Earlier this week, Fan visited the aircraft carrier USS Ronald Reagan and US military bases.
Wu Xi, deputy chief of mission at the Chinese embassy in Washington, said on Wednesday that Fans trip was aimed at preparing the way for a visit by Chinese President Xi Jinping in September.
China protested to the United States last month after a US spy plane with a television crew aboard flew close to artificial islands China has been building in the South China Sea.
The need for an understanding on air operations was shown last year when the Pentagon accused a Chinese fighter pilot of conducting a "dangerous intercept" of a US Navy patrol plane by flying a few yards from the U.S. jet and performing acrobatic maneuvers around it.