"We have noticed relevant reports and lodged solemn representation with the relevant side in the United States," Mr Shuang's statement reads.
"I must point out that there is only one China in the world and Taiwan is an inseparable part of the Chinese territory ... The 'one China' principle is the political foundation of China-US relations," he said.
"We urge the relevant side in the US to adhere to the 'one China' policy, abide by the pledges in the three joint China-US communiqués, and handle issues related to Taiwan carefully and properly to avoid causing unnecessary interference to the overall China-US relationship."
But unofficially, Chinese citizens have begun making their own commentary on Trump's call, along with "advice" over the controversial issue of the South China Sea.
Trump used a platform banned by censors in mainland China - Twitter - to renew several of his criticisms during the US presidential campaign. AP reports "some of his arguments aren't true".
Since the announcement of the phone call, he's taken to Twitter again to criticise those who choose to criticise him.
Since, relations seem to have soured further. The Global Times, one of state-run newspapers known to be used by China's Communist leadership to send messages abroad, tweeted messages from "netizens" offering their own advice.
"Why should China ask you if it is OK? Did the US ask China if it was OK to deploy THAAD (Terminal High Altitude Area Defense - a missile system) in South Korea and sell weapons to Taiwan?," One user wrote.
"Trump may need to employ the world's most powerful PR team, even Kissinger can't help him now," said another.
Meanwhile, in an editorial published overnight, the Times warned Trump "might be looking for some opportunities by making waves".
The piece, titled Talk to Trump, punish Tsai administration, said that "however, he has zero diplomatic experience and is unaware of the repercussions of shaking up Sino-US relations.
"The Trump-Tsai phone call has rocked and confounded the world.
"All US mainstream media have pointed out that the Taiwan question is among the most sensitive issues in East Asia, and any mishandling of it could lead to war. Trump's jaw-dropping move has raised many doubts about whether it is in line with the US' long-term interests."
The dispute between Taiwan and Beijing began when the losing side of China's 1949 Civil War fled to the island and continued to declare itself the rightful rulers of China. Military tensions have existed between the communist regime and Taipei ever since.
Last month, Mr Trump had a call with Chinese President Xi Jinping during which Mr Trump's office described him as saying he believed the two would have "one of the strongest relationships for both countries".
- Additional reporting by AFP and AP
