Beijing is trying to keep Taiwan isolated on the world stage and opposes countries having official exchanges with Taipei.
It claims self-ruled, democratic Taiwan as part of its territory to be seized one day, by force if necessary.
"Pavel... trampled on China's red line," said Chinese foreign ministry spokeswoman Mao Ning.
"This severely interferes in China's internal affairs and has hurt the feelings of the Chinese people," she added.
Beijing has urged Prague to "immediately take effective measures to eliminate the negative impact of this incident and avoid irreparable damage being sustained to China-Czech relations", Mao said.
Pavel, who won the presidential election on Saturday, will replace pro-Chinese incumbent Milos Zeman on March 9.
Earlier this month, Zeman held a 45-minute video call with Chinese President Xi Jinping, whom he calls his friend, and hailed "friendly relations" between the two countries.
Pavel then talked to Taiwanese President Tsai Ing-wen, who had congratulated him on his election win.
"I thanked her... and I assured her that Taiwan and the Czech Republic share the values of freedom, democracy and human rights," Pavel said on Twitter.
"We agreed on strengthening our partnership," added the former general, who served as head of NATO's military committee in 2015-2018.
He said he hoped "to have the opportunity to meet President Tsai in person in the future".
The Taiwanese presidential office said the call, which Taiwanese Foreign Minister Joseph Wu also joined, lasted almost 15 minutes.
"The president... acknowledged that president-elect Pavel carries on the spirit of former Czech president (Vaclav) Havel, who respected democracy, freedom and human rights, under which the republic was founded, and is like-minded with Taiwan," Tsai's office said.
Havel was the Czech Republic's first president, serving from 1993 to 2003.
Before Havel became head of state, the dissident playwright had in 1989 led the Velvet Revolution, which toppled Communism in the former Czechoslovakia.
Mao said Beijing was urging Prague to "earnestly abide by its political commitment to the One China principle" observed by the European Union.
In a radio interview on Sunday, Pavel said the one-China policy should be supplemented with a "two-system" principle.
"There is nothing wrong if we have specific relations with Taiwan, which is the other system," Pavel said.
burs-frj/gil
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