In a conversation that also covered trade, Macron expressed "his serious concern about stability in the region", a statement by the French presidency said.
Macron phoned Iranian President Hassan Rouhani on Wednesday, the day after Trump announced that the US was pulling out of the Iran nuclear accord, and assured him that France, Britain and Germany were still anxious to keep the deal alive.
European nations are to negotiate with the US over its threat to slap sanctions on companies that do business with Iran.
"We cannot let others decide for us," Macron has said, although experts say that the Europeans do not have much room to manoeuvre in this case.
EU heads of state are to make a declaration on the question on Wednesday in Sofia, on the eve of a summit on the Balkans.
Iranian Foreign Affairs Minister Javad Zarif started a tour of signatory nations this weekend.
After Beijing and Moscow, he was to visit Brussels on Tuesday to meet his French, British and German counterparts.
"We hope that with this visit to China and other countries we will be able to construct a clear future design for the comprehensive agreement," he told reporters after talks in Beijing with his Chinese counterpart Wang Yi.