Based on the integrated study of structure attributions and characteristics of the original basin in combination with lithology and lithofacies, sedimentary provenance analysis and thickness distribution of the Mesozoic Ordos Basin, it is demonstrated that the depocenters migrated counterclockwise from southeast to the north and then to the southwest from the Middle-Late Triassic to the Early Cretaceous. There were no unified and larger-scale accumulation centers except several small isolated accumulation centers before the Early Cretaceous. The reasons why belts of relatively thick strata were well developed in the western basin in several stages are that this area is near the west boundary of the original Ordos Basin, there was abundant sediment supply and the hydrodynamic effect was strong. Therefore, they stand for local accumulation centers. Until the Early Cretaceous, depocenters, accumulation centers and subsidence centers were superposed as an entity in the southwest part of the Ordos Basin. Up to the end of the Middle Jurassic, there still appeared a paleogeographic and paleostructural higher-in-west and lower-in-east framework in the residual basin to the west of the Yellow River. The depocenters of the Ordos Basin from the Middle–Late Triassic to the Middle Jurassic were superposed consistently. The relatively high thermal maturation of Mesozoic and Paleozoic strata in the depocenters and their neighborhood suggest active deep effects in these areas. Generally, superposition of depocenters in several periods and their consistency with high thermal evolution areas reveal the control of subsidence processes. Therefore, depocenters may represent the positions of the subsidence centers. The subsidence centers (or depocenters) are located in the south of the large-scale cratonic Ordos Basin. This is associated with flexural subsidence of the foreland, resulting from the strong convergence and orogenic activity contemporaneous with the Qinling orogeny.