During the conversation, Xi stressed that important results have been achieved in bilateral relations since his meeting with Trump in Florida in April.
But at the same, Xi said relations "have been affected by some negative factors" and the Chinese side has already expressed its position to the US, Chinese state media reported.
The Chinese president also said that his country attaches great importance to Trump's reaffirmation that the US will adhere to the 'One China' policy.
The two presidents also discussed the peace and stability of the Korean Peninsula.
"President Trump raised the growing threat posed by North Korea's nuclear and ballistic missile programmes. Both leaders reaffirmed their commitment to a denuclearised Korean Peninsula," the White House said in a statement.
"Trump reiterated his determination to seek more balanced trade relations with America's trading partners. The two leaders also discussed a range of other regional and bilateral issues of mutual interest, and affirmed that they look forward to meeting at the G20 in Hamburg, Germany," the White House said.
The conversation between the two leaders came a day after a US missile destroyer sailed close to an artificial island built by China in the disputed South China Sea. China termed the incident a "serious political and military provocation".
Trump on Thursday authorised a USD 1.3 billion arms sale to Taiwan, which China considers a rebel province. The same day, the US Treasury Department imposed sanctions on a Chinese bank accused of laundering North Korean cash.
Also on Thursday, the State Department expressed concern about Beijing's respect for freedom in Hong Kong, on the 20th anniversary of Britain ceding the territory back to China.
All those steps added up to a sharp reversal in tone from April, when Xi travelled to Trump's Mar-a-Lago resort for a first face-to-face meeting that Trump later said had helped build an "outstanding" relationship.
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