Abstract: The structure in southeast Sichuan is complicated, and there are abundant shale gas resources in Permian and Silurian strata. Based on the analysis of lithology and interpretation of seismic data, Cambrian gypsum-salt layer and Middle-Lower Triassic gypsum-salt layer had important control action to structural deformation, most faults sliped along gypsium-salt layer. The study area includes two parts:inner basin and basin margin. In inner basin symmetric folds with decollement of overlying strata were developed, basin margin was featured by structure of base-involved fold and thrust fault, and can be distinguished as piedmont nappe zone and piedmont conversion zone. High-steep triangle wedge was developed in piedmont nappe zone. Conversion zone can be divided into thrust belt, fold belt and slope belt. Analysis of structure evolution showed that in Late Jurassic Qiyueshan fault started developing, the strata in inner basin were bended and deformed. In Cretaceous triangle wedge was formed in basin margin, and main folds and faults had been already developed in inner basin. In Cenozoic Qiyueshan mountain was folded and uplifted, and several anticlines and synclines were formed in sedimentary cover above Cambrian in inner basin. In piedmont nappe zone, high-steep structure and intense deformation led to the poor preservation condition of shale gas. In piedmont conversion zone, moderate deformation led to the good preservation condition of shale gas, especially in fold belt. Due to the good sealing-capping property of gypsum-salt bed of Middle-Lower Triassic, anticlines with suitable burial depth are the favorable exploration targets.