Xi's message comes as bilateral ties have sunk to their lowest point since diplomatic relations were established in 1992.
He said bilateral exchanges and cooperation in various fields have yielded remarkable results and concrete benefits to the two nations, as well as positive contributions to regional peace and development.
On the basis of mutual understanding and mutual respect, China is committed to cementing political mutual trust, properly handling differences and enhancing coordination and cooperation, so as to push for the healthy and stable development of bilateral ties, he added.
"I would like to work with you to ensure the development of Sino-South Korean ties better benefits the two countries and peoples," the Chinese president said.
The bilateral relations have sunk to one of their lowest points recently over the deployment of the US Terminal High Altitude Area Defense (THAAD) missile defense system. China fears the system's radar could be used to monitor the Chinese military's flights and missile launches.
Moon won a landslide victory in the presidential by- election yesterday.