Abstract: The Junggar Basin is an important onshore petroleum-bearing basin in China, and the restoration of its strata denudation thickness is effective to study the evolutionary history and evaluate the oil-gas resources. By analyzing the principle and application conditions of interval transit time method, it is considered that the method is suitable for restoring the strata denudation thickness in the fault-depression transition period of Junggar Basin. The actual calculation results show that in the fault-depression transition period, there is a major unconformity between the Upper and Middle Permian with large denudation thickness, and a secondary unconformity between the Triassic and Permian, with relatively large basin denudation thickness, located in the western basin margin zone, with the denudation gradually decreasing from northwest to southeast and reaching the lowest level at the center of basin. Among the tectonic units, the convex suffered more denudation than the sag, reflecting that the ancient landform is high in the northwestern margin and low in the central basin, and the reformation of the basin is intense in the west and weak in the east, and intense in the margin and weak in the interior during the Late Permian-Early Triassic in Junggar Basin.