Wang Yi met the two leaders separately with both sides pledging to further promote relations between the two countries.
China said that US's action violates the basic norms of international relations and will aggravate regional tensions and turbulence.
China's officially atheist government is wary of any organised movements outside its own control, including religious ones.
The air strike was followed by an aerial combat between air forces of the two countries on February 27 when Pakistan jets entered India.
The 22nd meeting of special representatives of India and China for border talks will begin here on Saturday.
Wang's visit on Wednesday came after years of tensions over the U.S. Terminal High Altitude Area Defense (THAAD) system placed in southern South Korea and amid concerns that a U.S.
Will play 'constructive role' in improvement of India-Pakistan ties: Chinese Foreign Minister Wang Yi
Wang said that China's respective relations with India, Pakistan and other South Asian countries could run in parallel and develop together.
Foreign Minister Wang Yi avoided any references to the Kashmir issue as well as India's move to revoke the Article 370 in Valley.
External Affairs Ministry Spokesperson Raveesh Kumar said India expects other countries to respect India's sovereignty and territorial integrity.
China has told the General Assembly that the 'dispute' should be peacefully and properly addressed in accordance with the UN Charter, Security Council resolutions and the bilateral agreement.
The two sides are expected to sign two agreements related to educational and economic cooperation during the visit.
Chinese Foreign Minister Wang Yi's visit to Pakistan took place amidst fresh India-Pakistan tensions after New Delhi revoked Jammu and Kashmir's special status on August 5.
Foreign Minister Shah Mahmood Qureshi received Wang at the Noor Khan Airbase.
The sources said India has asked leaders of some other countries too not to come to New Delhi if they combined it with their trip to Pakistan.
Defence Minister Nirmala Sitharaman also landed in Beijing earlier on Tuesday to attend preparatory meetings with the External Affairs Minister on the sidelines of the SCO meeting.