Xi told Moon China had always upheld the denuclearisation of the Korean peninsula and that the nuclear issue should be resolved through talks, which were in everyone's interests, according to a state television report.
South Korea and the United States began deploying the THAAD system in March and it has since become operational. The two leaders also agreed to strengthen their alliance, the White House said.
China's president has set out his opposition to the deployment of a USA missile system, in his first discussion with the new South Korean leader. It said Moon told Abe that it was emotionally hard for South Koreans to accept the agreement.
On Friday, Russia's President Vladimir Putin told Moon in a phone call he was ready to play a "constructive role" in resolving North Korea's nuclear threat, South Korea's presidential office said.
The THAAD deployment was agreed upon by Moon's predecessor, conservative leader Park Guen-hye.
China also hopes the new South Korean government attaches importance to China's concerns and takes steps to promote the stable and healthy development of ties, Xi said, Reuters reported.
North Korea, which considers China its sole major diplomatic ally and economic benefactor, is also expected to send a delegation to the two-day meeting in Beijing, the Chinese foreign ministry has said.
After the obligatory congratulations, Japan is cautiously watching to see how relations with South Korea evolve under Moon, known for his tough stance on wartime history and territorial issues. China denies it has done anything to hurt South Korean businesses.
Moon's more conciliatory approach to North Korea adds to uncertainty in bilateral and trilateral cooperation with the United States, given Prime Minister Shinzo Abe's vocal support for Trump's increased pressure on the North. Moon opposes a 2015 agreement signed by Park that was heralded as a final settlement for Korean women who were among many sexually enslaved in Japanese military brothels before and during World War II. It has also been working to develop a nuclear-tipped missile capable of reaching the United States, presenting Trump with perhaps his most pressing security issue.
Mr Moon's position on Thaad is not yet completely clear - his comments have been ambivalent in the past. "We hope the new administration values cooperation with Japan and the USA and develops realistic security and foreign policies".