It is of scientific important to understand the spatial and temporal order of Cenozoic structure deformation in the Western Qaidam Basin，which can improve the study on the uplifting process of the Tibet Plateau，and it also provides a new method of“exploring oil based on structure”. In this paper，the latest seismic data，borehole data and core data acquired from the Western Qaidam Basin in the last few years were used to study the spatial and temporal order of structure deformation in the Cenozoic based on the growth strata analyzing method. Study results indicate that：①the overall structure deformation in the Cenozoic of the Western Qaidam Basin is getting younger from SW to NE；②the distribution of the tectonic deformation in the Cenozoic of the Western Qaidam Basin is stratified in the time domain and spatial domain，which was resulted from the progressive transformation of the structure displacement along the detachment surface；③the western part of Yingxiongling structure belt and the Kunbei and Wunan areas are the most favorable exploration areas. The eastern part of Alar and Yingxiongling structure belt and the northern part of the Western Qaidam Basin are the secondchoice，while the areas from Eboshan to Huanggualiang are risky.