The remarks were in line with China’s recent efforts to capitalize on tensions between the United States and the Philippines and draw Mr. Duterte’s government closer with promises of economic aid.
“There is a scramble to win over the heart and mind of President Duterte,” said Patrick M. Cronin, a senior adviser at the Center for a New American Security, a Washington-based policy research group.
The two leaders also discussed tensions in North Korea, with Mr. Xi reiterating China’s call for restraint and dialogue. Mr. Trump and Mr. Duterte also spoke about North Korea in their call on Saturday, White House officials said.
Since taking office last year, Mr. Duterte has upset the balance of power in Asia by vowing to cut some military and economic ties with the United States. At the same time, he has embraced China as an economic and security ally and acquiesced to Chinese demands to resolve territorial disputes in the contested South China Sea through direct talks rather than international arbitration.
This week, Mr. Duterte welcomed Chinese Navy ships to Davao City, where he served as mayor for many years. It was the first visit by the Chinese Navy in several years.
In the phone call, Mr. Duterte thanked Mr. Xi for allowing him to tour a Chinese missile destroyer during the visit, according to a statement on Wednesday from the presidential palace in Manila.
Relations between China and the Philippines were once seriously frayed over disputed territory in the South China Sea, a major waterway in which China has sought to expand its influence in recent years. But under Mr. Duterte, the tensions have eased.
In a possible sign of Mr. Duterte’s efforts to please Beijing, the Association of Southeast Asian Nations, which Mr. Duterte chaired this year, did not criticize China’s actions in the South China Sea in an official statement following a meeting in Manila last week.
Bonnie S. Glaser, senior adviser for Asia at the Center for Strategic and International Studies in Washington, said Mr. Xi might have been showing approval for the statement by agreeing to speak with Mr. Duterte.
“China has benefited greatly from the shift in Manila’s policy toward the South China Sea and Duterte’s friendly approach to Beijing,” she said.