The deep and shallow structural frameworks are quite different in the Qaidam Cenozoic basin according to a comprehensive interpretation of seismic and non-seismic data. In different stages, the basin sedimentation is controlled by different structural frameworks. The nearly E-W-trending structures controlled the basin sedimentation in the Paleogene and the NW-trending structures controlled the basin sedimentation in the Neogene. It is indicated that the Qaidam Cenozoic basin is a large superposed basin controlled by structures of different directions in different stage. The characteristics of structural deformation in the deep and shallow strata are different. The fault-block structure mainly develops in the deep strata with reverse basement faults. Decollement folds and faults develop in the middle-shallow strata and the normal faults developed in the core of anticlines are diagonal combination on the surface. The basin experienced multi-cycle sedimentary evolution and later deformations of various types. Different structure combination forms different structural reservoir model. It is very important to recognize these for oil and gas exploration in deep basins, especially for the concealed reservoir exploration.