With US President Donald Trump preaching "America First" and dismissing climate change, Western allies are struggling to find a common front at the gathering - unlike previous summits when differences were drawn along global north-south and east-west lines.
With Russian President Vladimir Putin, Turkey's Recep Tayyip Erdogan and Saudi King Salman in the volatile mix for the July 7th-8th power meet, the list of potential minefield issues include the Syrian war, the Ukraine conflict and the diplomatic shut-out of Qatar.
Trump's anti-immigration stance has also emboldened many of the EU's eastern ex-communist members which have obstinately opposed Merkel's pleas to accept larger shares of the refugees who have flocked to Europe.
"Merkel has called a summit between Europeans because there is a problem with the relationship with Trump," said a diplomatic source, speaking on condition of anonymity.
"It's necessary to ensure European cohesion because within the G20, it's complicated."
Besides the transatlantic faultline, "there is also a new European division growing between east and west," noted Jean-Dominique Giuliani, president of Paris-based think-tank Fondation Robert Schuman.
The differences were buried when wealthier EU members supported the east, at a time of "financial flows towards central and eastern Europe", he said, adding that "they are reappearing again on the question of refugees".
Threatening to deepen divisions, Trump will head to Warsaw for a summit of central and eastern European leaders, likely including Hungary's hardline Prime Minister Viktor Orban, a day ahead of the G20.
European affairs journal Euractiv asked: "How strongly do all these countries from Central and Eastern Europe feel about Trump? It's difficult to say.
"But as some EU countries shun him and others welcome him with open arms, Trump could become the wedge that drives the Union apart."
'Don't Trump our planet'
Merkel will address the German parliament Thursday morning, when she is expected to outline her priorities for the G20 meeting.
Her European guests - the leaders of G20 members France, Britain and Italy, as well as of summit guest countries the Netherlands, Spain and Norway - will then hold their own mini-summit, along with EU chief Jean-Claude Juncker and EU Council President Donald Tusk.
But even these broadly like-minded Europeans have very different relationships with Trump.
Britain's Theresa May, who is leading her country out of the EU, has been derided at home for seeking to curry favour with Trump, after she invited him for a state visit that sparked a national outcry.
France's new President Emmanuel Macron, who had been dubbed an anti-Trump by some with his strong push-back against Trump's climate-sceptic stance, this week invited the US president to attend July 14th Bastille Day celebrations.
"With Macron, France is back, there is a re-balancing that was necessary with the relationship with Germany," noted Giuliani.
Ahead of the meeting, German Foreign Minister Sigmar Gabriel stressed the importance of Europe facing up to the US confidently.
"The German government does not have an anti-US strategy, but in America, there are strategists who are planning an anti-Europe, anti-German agenda," he noted.
"We do not want to forcefully separate the US from Europe. But what we don't want either is to appear like an appendage of US policies," he said.
Meanwhile, environmental activists urged the European leaders to take the lead in protecting the climate, as they called a demonstration on Thursday morning outside the chancellery where Merkel will receive her colleagues.
The protesters have pledged to turn up dressed "as the most important summit leaders in climate hero costumes with a three-metre high globe and a clear call to the G20: "Don't Trump Our Planet!"