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Abstract: Tectonism is one of the dominant factors affecting the shale pore structure. However, the control of shale pore structure by tectonic movements is still controversial, which limits the research progress of shale gas accumulation mechanism in the complex tectonic region of southern China. In this study, 34 samples were collected from two exploratory wells located in different tectonic locations. Diverse experiments, e.g., organic geochemistry, XRD analysis, FE-SEM, low-pressure gas adsorption, and high-pressure mercury intrusion, were conducted to fully characterize the shale reservoir. The TOC, Ro, and mineral composition of the shale samples between the two wells are similar, which reflects that the shale samples of the two wells have proximate pores-generating capacity and pores-supporting capacity. However, the pore characteristics of shale samples from two wells are significantly different. Compared with the stabilized zone shale, the porosity, pore volume, and specific surface area of the deformed zone shale were reduced by 60.61%, 64.85%, and 27.81%, respectively. Moreover, the macroscopic and fine pores were reduced by 54.01% and 84.95%, respectively. Fault activity and uplift denudation are not conducive to pore preservation, and the rigid basement of Huangling uplift can promote pore preservation. These three factors are important reasons for controlling the difference in pore structure between two wells shales. We established a conceptual model of shale pores evolution under different tectonic preservation conditions. This study is significant to clarify the scale of shale gas formation and enrichment in complex tectonic regions, and helps in the selection of shale sweet spots.