Ordos Basin, rich in multi-energy resources of oil, gas and uranium, is a depression basin within the Late Triassic-to-early Cretaceous craton, which overlapps on the Paleozoic craton basin. The basin started its later reformation in the Late Cretaceous, which is of significant importance to energy deposits. Few studies have, however, been focused on ages of the reformation and its characteristics. Based on the analysis of the regional geological settings and Cenozoic sedimentary structures, combined with published and newly developed fission track ages, the reformation was divided into five stages with various characters, including 1) regional uniform uplift stage (Late Cretaceous to Paleocene); 2) different uplift and subsidence stage (Eocene to Oligocene); 3) different uplift stage of the east and west of the basin (Early-Middle Miocene); 4) structural reverses of the east and west of the basin (Late-Miocene to Pliocene); and 5) the formation of loessial plateau and the development of the Yellow River (Quaternary). These stages are consistent with development of the regional tectonic settings, which is closely related to the subduction of the Pacific Block to Euro-Asian Block and the collision of Indian Block to Euro-Asian Block. It has been indicated that there are good correlations among the petroleum formation, migration and the mineralization ages and the reformation ages. The later structural uplift, on the one hand, caused the strata erosion and the destruction of the petroleum pools and also the dissipation of the oil and gas. On the other hand, it decreased the pressure causing the escape of the gas dissolved in water, which is helpful to formation of the complementary gas resource and the secondary petroleum pools. Meanwhile, the later uplift and the petroleum migration to the northeast enabled the organic and inorganic interaction between reducing fluid and ore-bearing fluid, which is preferable for uranium deposits. The uplifted and eroded Mesozoic strata could be a new provenance, resulting in new mineralization and overlapped enrichment of uranium deposits.