Greeting South Korean presidential envoy Lee Hae-Chan in Beijing, Foreign Minister Wang Yi said bilateral relations have made immense progress over the years.
"But this year we've had some undeserved setbacks," Wang said, likely in a veiled reference to the Terminal High Altitude Area Defense system that became operational earlier this month.
"We hope the new government will correct the problems that we have encountered and take effective measures and positions as soon as possible to remove the obstacles that have been placed on the road to good relations between our two countries."
South Korea's new President Moon Jae-In dispatched Lee to Beijing in the wake of his election victory last week.
Ties between Seoul and Beijing soured before Moon's election over the deployment of THAAD, which is aimed at guarding against threats from nuclear-armed North Korea.
China sees THAAD as a threat to the regional security balance.
Left-leaning Moon and President Xi Jinping spoke on the phone last week and both agreed that denuclearising North Korea was a "common goal" between them, Moon's spokesman said.
"We believe South Korea will bring clear measures to improve relations," Wang said.
For his part, Lee said Moon asked him "to express his thanks to President Xi for his message of congratulations after our election. He also asked me to come and engage in deep dialogue."
Moon's spokesman, Yoon Young, said last week that the special delegation to Beijing would "exclusively discuss the THAAD and the North's nuclear issues."
Moon, who took office on Wednesday, favors engagement with the North to bring it to the negotiating table over its nuclear and missile ambitions.
The United Nations Security Council met on Tuesday to discuss tightening sanctions on North Korea.