Duterte is loosening the Philippines' long alliance with the United States while strengthening ties with China and Russia, saying this week he might turn down an invitation from President Donald Trump to visit the US.
The call came two days after Duterte toured a visiting Chinese warship on the southern Philippine port of Davao in a display of warming ties with Beijing.
"The mutual political trust (between China and the Philippines) continues to grow and our cooperation is flourishing in all areas," Xi said, according to Chinese state media.
"Channels of dialogue and negotiation on the South China Sea issue have also been set up, which will benefit the fundamental interests of our two countries," he said.
In contrast to his predecessor Benigno Aquino, Duterte has pursued close relations with China despite its extensive island-building in disputed parts of the South China Sea.
China claims nearly all of the strategically vital waterway, even waters approaching the coasts of its neighbours, despite partial counter-claims from several regional states such as the Philippines.
Duterte has secured promises of billions of dollars' worth of investments from China in return for the diplomatic realignment.
Aquino in 2013 took China to a United Nations-backed arbitration tribunal over the maritime row.
The tribunal last year rejected China's claim over most of the South China Sea, but Beijing has ignored the ruling.
Duterte vowed after his election last year not to "taunt or flaunt" the ruling, saying he did not want to go to war with China.
On Monday the Philippine leader said he could not commit to visiting the US president because of a busy schedule, even though no firm date has yet been proposed.
Nevertheless, Duterte said relations with the United States were improving now that Trump had taken over from Barack Obama, who criticised the Philippine president for his anti-drug war that has claimed thousands of lives.
Rights groups have warned Duterte may be orchestrating a crime against humanity, with police and vigilantes committing mass murder, and Trump's invitation has stirred controversy in Washington.
Duterte denies his government is committing extrajudicial killings.
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