The Reagan administration's No. 2 trade negotiator, David R. Macdonald, resigned his position yesterday as deputy U.S. trade representative to return to the private practice of law.

No reason was given for the resignation of Macdonald, who held the rank of ambasssador and was described by the Office of the U.S. Trade Representative as "the administration's point man" in the tough trade negotiations with Japan.

Private trade attorneys and sources on Capitol Hill said Macdonald's resignation had been rumored, but they saw no major policy differences between him and the administration.

U.S. Trade Representative William E. Brock praised Macdonald's service and said his resignation was accepted "with my most profound regret, but with my deep personal appreciation and respect."

Macdonald will be returning to the Chicago law firm of Baker & McKenzie, working on international trade issues in its Washington office. Macdonald's resignation takes effect March 31.

His departure comes at a time when the Reagan administration is seeking ways to improve its handling of international trade issues, which have grown increasingly more important in the past year. America's growing trade imbalance with Japan dominated the just-completed visit of Prime Minister Yasuhiro Nakasone. China has made a major issue of U.S. quotas on textiles, retaliating by cutting its purchases of U.S. goods. And America's relations with its closest European allies have been damaged by three major trade disputes in the past four months.

According to administration and Capital Hill sources, no decision has been made yet on the form of the reorganization, though there are reports that three of the top players--Brock, Commerce Secretary Malcolm Baldrige and White House Counselor Edwin Meese III--have agreed that some action is needed.

One administration proposal is a merger of the Commerce Department International Trade Administration with the White House Office of the U.S. Trade Representative. It remained unclear, however, which office would be in charge of trade policy if that plan is accepted.