Macron's election "gives us the possibility to infuse a new dynamism into Europe's development", Merkel said after a meeting of her Christian Democrat party ahead of Macron's visit.
But the new French president's proposals of a eurozone parliament, budget and finance minister, and even a revised basic treaty, look set to run into German opposition.
Citing European Commission chief Jean-Claude Juncker, German finance ministry spokeswoman Friederike von Tiesenhausen said that such major reforms would require changes to the EU's main treaty, which would require the support of all 28 eurozone countries.
That is "at the moment not realistic", she said.
Foreign Ministry spokesman Martin Schaefer also said: "There is agreement within the government that, given the difficult situations we in Europe are confronted with, a plan with treaty changes is not a good idea."
Wurst and sympathy
Merkel, who was the first foreign leader to welcome Macron's election, said she would approach their meeting with "an open mind and great sympathy", stressing her "total confidence" in his capacity to improve France's situation.
For Berlin that means above all reducing France's deficit to the EU target of three percent of GDP, a prerequisite - not only for France but for other "southern European" countries - for discussing a common budget.
For their part, Macron and his allies are enthusiastically pro-EU, having fought off Eurosceptic Marine Le Pen in the presidential election.
There will be no "showdown" with Berlin, MEP Sylvie Goulard, a Macron ally who is tipped as a possible minister, said on Monday, arguing for a "cooperative approach" to defending France's interests.
Security, investment and social rights are likely to come up at the meeting, according to sources close to the president.
One question that attracted much attention in the French presidential election was that of posted workers - employees from one EU country working in another, whose employers can pay social contributions in their country of origin, which they might choose to do if they are lower.
French politicians say this leads to "social dumping" and Macron pledged to tackle the question.
The European parliament is supposed to be working on reforms, despite the opposition of east European countries, and may propose minimum contributions, limits on the length of postings and a ban on several postings in a row from different countries.
Macron has also proposed a Buy European Act, which would give priority to European companies in the attribution of public-sector contracts.
He also wants closer European cooperation on defence, especially because US President Donald Trump is not keen on Nato and may pull troops out of Europe, and a Franco-German digital investment project.
Lunch with Trump
Macron will meet Trump on 25 May for a "lengthy" get-to-know-you lunch, senior US adminstration officials said on Monday.
Trump will be in Brussels for a Nato summit, a source of contention since he wants European countries to raise their financial contributions to the defence alliance to two percent of GDP and reduce the US's commitment.
Although Trump issued a tweet praising far-right candidate Le Pen's position on border control during the presidential elecetion, Trump has been "very impressed" by Macron, according to an anonymous White House official, in particular by his 66.1 percent share of the vote in the deciding round of the presidential poll.
Before then Macron will visit French soldiers in Mali, where they are part of the Barkhane operation that is fighting armed Islamists in the north of the country, a further show of his support for the military following his visit to seriously wounded troops in a military hospital on Sunday after his swearing-in.