Underlining Beijing's challenges in getting Europe onside, news broke on the eve of the summit that Italy -- the bloc's third-largest economy -- had withdrawn from its vast Belt and Road infrastructure initiative.
China and the EU have ramped up diplomatic engagement this year in an attempt to repair damaged ties.
In opening remarks, Von der Leyen, flanked by European Council President Charles Michel and EU foreign policy chief Josep Borrell, told Xi "there are clear imbalances and differences that we must address".
"At times our interests coincide," she said, pointing to EU-China cooperation on artificial intelligence and climate change.
"When they do not, we need to address and responsibly manage the concerns that we have," she said.
Michel, in turn, said the bloc was seeking a "stable and mutually beneficial" relationship with China.
A day before the meeting in Beijing, Italy said it had formally withdrawn from the BRI, a central pillar of Xi's bid to expand China's clout overseas.
Prime Minister Giorgia Meloni has long been opposed to Italy's participation in an initiative viewed by many as an attempt by Beijing to buy political influence -- and whose economic benefits to Rome were limited.
Asked about that decision on Thursday, Beijing slammed the "smearing" of the project.
- 'Zero trust' -
The EU hopes meetings on Thursday will also provide a chance to discuss areas of common interest.
In his opening remarks, Xi urged his European visitors to "jointly respond to global challenges".
But other touchy topics are on the agenda, from human rights to the yawning EU-China trade gap.
And in talks with Premier Li Qiang Thursday afternoon, Von der Leyen reiterated her concerns about that "imbalance".
"We have to address the root causes for that and handle the resulting impact," she told Li.
The bloc was keen to "deepen our cooperation whenever possible and to manage our differences when it's necessary", Michel also told the Chinese premier.
Following their meeting with Li, Von der Leyen and Michel will attend an official dinner and a news conference in the evening.
European officials have said repeatedly this year they aim to "derisk" their economic ties to China after the war in Ukraine exposed the continent's energy dependence on Russia.
Beijing's goal this week will be to "hinder or delay derisking at a minimum cost", Grzegorz Stec, an analyst at China-focused think tank MERICS, told a media briefing Wednesday.
Also on the agenda at the summit will be the fighting between Israel and Hamas -- as well as Russia's war in Ukraine.
China, which has not condemned Moscow's February 2022 invasion of its neighbour, welcomed Russian President Vladimir Putin to Beijing in October, with Xi hailing their "deep friendship".
Such camaraderie is unlikely in Thursday's talks with EU leaders, who one analyst said had "zero trust" in Beijing.
"Both sides are unlikely to get what they want from the other side," Nicholas Bequelin, a senior fellow at Yale's Paul Tsai China Center, said.
The Europeans have said they will urge Beijing to use its ties with Moscow to push it to end its war against Ukraine.
But speaking to journalists on Thursday evening, one Chinese foreign ministry official suggested Beijing would not be able to sway Moscow.
Russia "is a very independent sovereign nation", Wang Lutong, director general of the Chinese foreign ministry's European department, told a press briefing.
"President Putin is making his decision based on his own national interest and security," he said.
He also said he believed that Beijing "could not be held accountable" for the imbalance in trade.
"We are very keen to importing more [products] from Europe, particularly high advanced technologies and high valued products," Wang said.
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