The visit to the Pentagon of General Fan Changlong, vice chairman of China's Central Military Commission, was relatively low key amid simmering tensions over the maritime dispute and a massive hack of US federal employees.
China insists it has sovereignty over nearly all of the South China Sea, a major global shipping route believed to be home to oil and gas reserves, but rival claimants accuse it of expansionism.
Carter had previously accused China of being out of step with international rules in its conduct in the South China Sea.
Unlike previous trips, including one last year, there was no joint press conference.
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"The Chinese did request that there not be a lot of media attention around this trip," Pentagon spokesman Colonel Steven Warren said.
The vast cyberattack is suspected to have originated in China, though Beijing has said the charge was "irresponsible" and stressed that Chinese laws prohibit cybercrimes.
Prior to visiting Washington, Fan went to California and Texas.
His trip is part of a years-long effort to build a regular dialogue between the American and Chinese armed forces to defuse potential tensions and avoid miscalculations.
Carter's predecessor, Chuck Hagel, visited China in 2014 in a trip that was marked by friction, with each side trading sharply worded criticism.