Wen told visiting President Lee Myung-bak that the countries must seize the moment to deepen East Asian economic integration.
"China and South Korea need to grasp the opportunity, closely communicate and coordinate, and initiate bilateral free trade agreement negotiations as soon as possible," Wen said.
He also said China and South Korea needed to begin talks with Japan this year "to promote the process of creating a free trade area between the three countries and the Association of Southeast Asian Nations (ASEAN)".
South Korea's Lee agreed. "Signing a bilateral free trade agreement and promoting East Asian cooperation suits the joint interests of both countries. South Korea is willing to diligently strive with China toward common goals," he told Wen on the second day of a three-day state trip to China.
Chinese media had said on Monday that closer economic ties brought by a possible free trade deal would help to narrow political distrust, as Beijing has faced growing wariness from neighbours over its military modernisation and strategic intentions.
In late December Japan and China agreed to start formal talks early this year on a free trade pact that would also include South Korea.
The resurgence of interest in the trade pacts follows Washington's push for a Trans-Pacific Partnership (TPP) trade agreement in November, which excludes China.
Japan had said at the Asia Pacific Economic Cooperation summit in Honolulu in November that it wanted to join in the talks over the U.S. proposal.
However, some people in China see the TPP as a political move by Washington to isolate Beijing on trade with Asia's biggest economies.
Still, trade talks between the major Asian economies have long been in the works, and South Korea and China have held a series of joint feasibility studies on a possible free trade deal since 2008.
Wen and Lee also held "candid and in-depth" discussions on the security situation in Northeast Asia, China's official Xinhua news agency said without elaborating.
Lee's office said in a statement after his meeting with Wen that the two "shared the view that denuclearisation of the Korean peninsula as well as peace and stability are of paramount importance and agreed to continue to closely consult and cooperate with each other".
Since North Korean leader Kim Jong-il's death last month, Beijing has called on regional powers to press ahead with efforts to restart aid-for-disarmament talks with Pyongyang.
South Korea had said talks to preserve stability on the peninsula would be a priority during the trip as the unpredictable North undergoes a delicate transition of power to Kim's largely unknown youngest son Kim Jong-un. (Reuters)
