In recent years, the exploration and development of unconventional oil and gas resources in China have developed rapidly, and commercial exploitation has been achieved in the Sichuan basin and other shale gas bearing basins. With the gradual depletion of shallow resources, deep shale gas resources have become a new exploration hotspot, and new requirements for accurate prediction have also been put forward. In exploration practice, the data and experience formed by the study of mid-shallow shale reservoirs are difficult to apply in deep shale, leading to difficulties in heterogeneous predicting. In this study, multiple experimental methods were used to make genesis-structure interrelated characterization of nano-scale pores in the Wufeng and Longmaxi formation shale reservoirs. Representative samples were selected from deep shale wells in the western Chongqing area, and methods of argon--ion polishing-field emission scanning electron microscopy (FE-SEM), energy spectrum, high-pressure mercury intrusion, and low-temperature nitrogen gas adsorption were applied for comprehensive research. The research results established the relationship between the genesis and structure of different types of pores, and summarized the combination and characteristics of pore types in different stages of the reservoir. On this basis, this study has developed a new approach for characterizing and evaluating reservoir pores based on the unit of "pore-system". 6 different pore-systems were identified within the Wufeng and Longmaxi formation shale reservoirs, and the particularity of high-quality reservoirs at the Wufeng Formation and the bottom of Longmaxi Formation was revealed. Genesis-structure interrelated characterization reveals the structural specificity of pores of different genetic types, which can provide scientific basis for predicting reservoir properties and gas content.