An extensive shift of ambassadors will mean new faces at the top of one-third or more of the 139 U.S. missions abroad in the coming year, State Department sources said yesterday.

In one of the earliest and most prominent shifts, veteran diplomat Thomas R. Pickering is slated to move from his hot spot in El Salvador to another of vital importance, the U.S. Embassy in Israel.

Pickering, who served a decade ago as ambassador to Jordan, is said to be Secretary of State George P. Shultz's choice to succeed Samuel W. Lewis at the Tel Aviv embassy. The highly respected Lewis has been in the job for nearly eight years, since the beginning of the Carter administration. He had planned his retirement for some time, and his uncharacteristic public criticism of President Reagan's Middle East peace plan shortly before the election guaranteed it.

Senior State Department officials denied reports that Pickering is leaving San Salvador because of concern for his safety. The dominant reason for the shift is that Shultz wants him someplace else, an official said.

A major turnover of ambassadors is common at least every four years, according to an official involved in preparing the current change. This time, he said, a more systematic approach is being sought in order to consider many moves on the diplomatic chessboard at one time. One aim is to broaden the experience of career ambassadors through a diversity of assignments in various regions.

Another factor is the large number of senior career officers who are in line for ambassadorships but do not have them. The large-scale change will ease the plight of some of the "hall walkers" who are looking for embassies of their own.

U.S. ambassadors who have been in their positions for three years are likely to be changed in the absence of special circumstances, according to officials. A hardship post, especially one involving substantial personal danger, is likely to be turned over in two years or less.

News service reports said ambassadorial changes are likely in Bolivia, Chile, Costa Rica and Honduras as well as El Salvador, giving rise to speculation about a new upheaval in the Latin American bureau, which went through a shakeup at the beginning of the Reagan administration.

A senior official, denying any ideological or political dimension, explained that the first in a series of regional studies about ambassadorial changes focused on Latin America. Studies and recommendations about other regions are to follow.

The State Department hierarchy is still unsure how much pressure will be exerted from White House political circles for the appointment of non-career ambassadors. The test of State's and Shultz's clout is not likely to be long in coming. About a dozen of Shultz's ambassadorial recommendations are already at the White House. More recommendations are going forward to 1600 Pennsylvania Avenue nearly every day.