The EU wants to levy tariffs on Chinese solar panels and phone gear amid claims they are unfairly undercutting rivals.
Chancellor Merkel now wants "intense" talks between the EU and China.
She was quoted as saying that Germany would use its position of power within the EU to ensure that the talks were productive.
According to the Associated Press news agency, she said that Germany would work for the issues to be resolved as quickly as possible because she did not believe that tariffs would help either side.
"We should very intensely use the next six months, and Germany will do everything to ensure that the talks will really advance," she explained.
Mr Li and Mrs Merkel were meeting as part of the Chinese leader's first overseas tour. Before Germany, he had already touched down in India, Pakistan and Switzerland.
China's premier has been warning that any attempt to impose tariffs would be seen as protectionist and ultimately hurt consumers.
"This decision will not only harm jobs in China, as well as development in the affected industries, but it will also affect development and endanger industry in Europe," he told a press conference in Berlin.
The probe into whether China has been selling solar products below cost is the biggest ever undertaken by the EU.
EU Trade Commissioner Karel de Gucht has proposed taxes averaging 47% on solar imports and a decision is expected next month.
The EU is also investigating subsidies provided to China's telecoms sector.