Liu expressed concern about US tariffs and sanctions, and its treatment of Chinese companies, the statement said.
Relations between Beijing and Washington nosedived under former president Donald Trump, who imposed tariffs on Chinese products worth billions of dollars in 2018, citing trade practices he deemed as "unfair."
After Joe Biden took power in January, he launched a review of the US trade strategy and tariffs initiated by Trump.
But his administration also says that China's massive state subsidies for national companies, intellectual property theft and other factors create a heavily uneven playing field in trade.
According to a readout of the call from the US treasury, Yellen "frankly raised issues of concern" in the meeting and the two sides recognised that "developments in our two economies have important implications for the global economy".
Earlier this month, US trade representative Katherine Tai spoke to Liu for a second time to discuss Chinese commercial practices.
Last week China promised the World Trade Organization it would further open its vast market, with a swift counter from Washington that it believed Beijing showed "no inclination to change".