Unconformities are of significant interest to petroleum geologists because of their crucial roles in influencing reservoir quality and controlling oil and gas migration. This study investigates the impact of unconformities on a reservoir within a prolific oil–gas-bearing zone between the Middle Permian and Lower Triassic strata in the northwestern Junggar Basin, utilizing thin sections, well logging data, seismic profiles, and geochemical analyses. The results reveal a well-developed three-layer unconformity structure characterized by a thick weathered clay layer, which acts as an effective caprock for hydrocarbons. The diagenetic evolution of the Lower Wuerhe Formation in the northwestern Junggar Basin consists of an initial stage of compaction followed by a subsequent stage of dissolution and cementation. Four key factors, including low argillaceous content in sandstone and conglomerate, diagenetic compaction, zeolite dissolution and cementation, and clay mineral infill, have played a crucial role in influencing the reservoir characteristics of the Lower Wuerhe Formation. In addition, the development of unconformities promotes atmospheric freshwater leaching, which enhances the dissolution of the underlying reservoir while developing an extensive network of strike-slip faults that improve connectivity within hydrocarbon reservoirs. This process facilitates both vertical and lateral migration of hydrocarbons along hard rock layers, which allows the unconformity to breach into the overlying conglomerate reservoirs. The results of this study suggest that the reservoir in proximity to the unconformity surface often exhibits high porosity and rich hydrocarbon content, offering valuable insights for future oil and gas exploration and development.