Clinton told Xi that he cherished relations between the US and China, which feature sincerity, mutual trust and constructive cooperation.
He congratulated Xi on the success of the recent Plenum of the Communist Party of China (CPC) and voiced support for China's comprehensive and deepening reform, state-run Xinhua news agency reported.
The plenum has endorsed reforms to give wider role for markets and private capital, providing a level playing field between private sector and state-owned enterprises.
Xi applauded Clinton's efforts to promote bilateral ties during his tenure and his cooperation with China after his retirement in efforts related to poverty reduction, charity, health and epidemic prevention, particularly in the area of HIV-AIDS.
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Despite ups and downs, Sino-US ties have generally moved in the right direction and yielded fruitful results, Xi said.
"With the joint efforts of generations of Chinese and US leaders, our relationship has become a skyscraper. We need to work together to do more to help the relationship."
He said the two sides are enhancing cooperation in politics, trade, ecology and people-to-people and cultural exchanges and will work together to cope with challenges regarding climate change and energy security.
As long as both sides adhere to the principles of establishing a new type of relationship between major countries, respect each other and achieve win-win cooperation, bilateral ties will have broader prospects, Xi noted.