Trump may have vowed to pull the US out of the 2015 climate protection deal, but "many many other countries want to go on implementing" it, Merkel told journalists.
Efforts to halt climate change is a key issue that world leaders gathering from Friday in the German port city of Hamburg are struggling to find consensus on.
Merkel has said that the talks on the issue would "not be easy" with Trump, who has once called climate change a Chinese hoax.
"We are not going to paper over the differences but rather, we will call discord discord. Because there are also different opinions on some important questions," she said.
In the run up to the summit, negotiators from the 20 world powers have already been battling for days to lock down an agreement for a final communique.
Sources close to negotiations say the G20 final document -- to be finished by Saturday morning -- would reflect the 19-versus-US situation, underlining that the Paris accord is "irreversible".
It would also reaffirm that other G20 nations are committed to the Paris accord while "taking note" of Washington's decision.
Earlier fears that some G20 members such as Saudi Arabia could be tempted to side with the world's biggest economic power have not materialised, said a source speaking on condition of anonymity.
German Foreign Minister Sigmar Gabriel said after Merkel's talks with Trump said that Germany and the US remained "significantly at odds" on climate as well as over trade.
"The question is whether the Americans remain convinced that the only thing that counts on global trade is whether America is the winner or not," Gabriel told public broadcaster ARD.
"Or can we manage to convince the Americans that if everyone plays by the same rules, then this will be best for everyone," he said.
Signing up to an anti-protectionist pledge used to be routine at G20 meetings, but not this time, with Trump reportedly eyeing tariffs on steel imports as he seeks to put "America first".
Sources close to the negotiations on the final communique said that the US was unlikely to agree to a strong condemnation of protectionism.
Instead, they said that the statement might stress the importance of free trade but also recognise the right of countries to defend itself against uncompetitive practices.
"This would be a first," one source said.