Abstract: With the continuous exploration and development of shale gas in China, the complex structure area has become an important direction for further exploration. The Longmaxi shale samples collected from complex structure area in Northeast Chongqing were conducted scanning electron microscopy, mercury intrusion, low-pressure gas adsorption, isothermal adsorption. This study systematically characterized the pore structure and adsorption capacity of Longmaxi shale in different tectonic belts, analyzed the influencing factors of pore structure and adsorption capacity, and revealed the action mechanism of tectonic deformation on pore structure and adsorption capacity. The results showed that ① OM pores are relatively developed in the Longmaxi shales collected from thrust slip belt and thrust fold belt, but not in the Longmaxi shale from imbricate thrust belt, where mineral-related pores and fractures are mainly developed. ② Micropores (<2 nm), mesopores (2~50 nm) and macropores (>50 nm) are developed in the Longmaxi shale in the thrust slip belt, while mesopores and macropores are relatively developed in the thrust fold belt and imbricate thrust belt. ③ The “excess” adsorption capacity of Longmaxi shale rapidly increases with the increased pressure, and slowly decreases after reaching the maximum (6−9 MPa), while the absolute adsorption capacity monotonously increases with the increased pressure. ④ The pore structure is mainly controlled by TOC (Total Organic Carbon) and clay mineral content, and the adsorption capacity is closely related to TOC and micropores. In addition, tectonic deformation can also affect the adsorption capacity by modifying the pore structure. This study has a very important guiding significance for the evaluation and development of shale gas resources in complex tectonic areas.