The 39-year-old former economy minister, who has surged from outsider to a frontrunner ahead of polls in April and May, said after an hour-long meeting with Merkel in Berlin that he aimed if elected to strengthen ties with Germany.
"I haven't forgotten I am only here as a candidate but I saw a lot of common ground with the chancellor, as well as a lot with President (Frank-Walter) Steinmeier," he told reporters outside her chancellery after whirlwind talks during his one-day visit.
Macron had already visited Berlin in early January but did not meet Merkel, widely seen as Europe's most influential leader.
The chancellor had received Macron's rival, conservative former prime minister Francois Fillon, in late January, just before a French newspaper alleged that he paid his family for fake jobs while in parliament.
Fillon was charged Tuesday with misuse of public funds and other offences and has since tumbled to third place in the polls ahead of the first round on April 23.
In private, close associates of Merkel have expressed astonishment that Fillon has stayed in the race even as his legal problems mount.
In 2012, Merkel had kept then-presidential candidate Francois Hollande, now France's president, at arm's length, instead throwing her support behind incumbent Nicolas Sarkozy.
That came later to be seen as a mistake in Berlin as it got the relationship off to a rocky start.
Macron, who is running as a centrist independent for his new "En Marche" (On the Move) movement, and the anti-establishment Marine Le Pen are shown in opinion polls to be the likely top two candidates after the first round.
He has campaigned on the type of sweeping changes to the French economy that Berlin has long championed and implemented more than a decade ago.
On Thursday he said he and the German leader had discussed "my willingness to reform our labour market, our education system and to have a sensible fiscal consolidation, an investment package for our economy and to respect our commitments".
"I spoke to someone (Merkel) who was very open to an even closer Franco-German partnership, particularly at a moment in which Europe is facing key changes" including Britain leaving the EU, Macron added.
Merkel did not comment on the informal meeting, in keeping with official protocol.