The total organic carbon (TOC) content and thermal evolution maturity of the Longmaxi Formation shale in the complex tectonic area of the southeastern Sichuan Basin are high, but the tectonic conditions are complex. There are few studies on the microscopic pore structure characteristics and fractal characteristics of the Longmaxi Formation shale, which are different from the shale in the Sichuan Basin and need to be further studied. In order to better characterize the heterogeneity of shale pore structure and its influence on shale gas enrichment, nuclear magnetic resonance, high-pressure mercury injection and scanning electron microscopy were used to quantitatively characterize the microscopic pore structure characteristics of shale in complex structural areas. Based on the fractal theory, the fractal dimensions of pores with different scales were obtained by high pressure mercury intrusion and nuclear magnetic resonance. The relationship between fractal dimension and pore throat structure parameters, TOC content and mineral composition content and its geological significance were discussed. The results show that organic pores, intergranular pores and micro-fractures are mainly developed in the shale of complex structural area in southeastern Sichuan Basin. The pore structure has multifractal characteristics, and the fractal dimensions of pore throats at different scales are different. The complexity of large pore throats is higher than that of small pore throats. The total fractal dimension of pores is 2.4702~2.8191, with an average of 2.6256. It reflects that the shale in the complex structural areas develops more complex pore structure, provides a large number of adsorption points for shale gas, and has a positive effect on shale gas accumulation. The combined effects of TOC content and quartz content result in strong heterogeneity and complex pore structure characteristics of shale in the study area. Compared with the shale in the Sichuan Basin, the shale in the study area has wide pore size distribution and low fractal dimension. Comprehensive analysis of shale pore structure and fractal characteristics can provide an important reference for the optimization of favorable shale reservoir sections in Zhaotong demonstration area and even the whole Sichuan-Chongqing basin margin.