Marine shale gas in the southern Sichuan Basin is the most successful area of shale gas exploration and development in China. In order to open up new shale gas fields and search for new shale gas reserves and production replacement blocks, it is necessary to continuously establish and complete the standards on shale gas reservoir evaluation and area selection under different structural settings. The early exploration practice shows that shale in the mountainous complex structural area along the southwestern margin of the Sichuan Basin varies greatly in the gas bearing property, so systematical analysis and study on the shale gas enrichment mechanisms in this area is of great significance to searching for new shale gas exploration areas. Based on drilling data of 5 wells in the mountainous complex structural area along the southwestern margin of the Sichuan Basin, the main factors controlling the shale gas bearing property and the shale gas enrichment model were discussed based on the systematical experiments and analysis of the outcrops, cores and cuttings of Longmaxi Formation shale from the aspects of organic geochemistry, physical property, gas content, hydrocarbon generation history and pore evolution history, so as to lay a solid geological basis for the birth of a new shale gas area. And the following research results were obtained. First, the shale of the first submember of first Member of Longmaxi Formation (S1l11) in the mountainous complex structural area along the southwestern margin of the Sichuan Basin has an average TOC of 3.02%–4.97% and Ro of 2.38%–3.37%, and the average total gas content in local enrichment zones is up to 4.62 m3/t, so it is classified as quality shale. Second, the detailed studies on hydrocarbon generation history indicate that the shale has the characteristics of “low thermal evolution rate and low maturity”. It is characterized by late hydrocarbon generation, low thermal evolution rate, low current maturity and short late diffusion time, which are favorable for shale gas enrichment. Third, the pore evolution history reveals that shale pore evolution can be divided into six stages, i.e., sharp pore reduction, pore reduction, organic pore formation, pore preservation, organic pore dissipation and karstification, and organic pore and TOC are the most direct control factors of shale gas content. Fourth, favorable shelf facies belt is conducive to the formation of large-scale reservoir space and effective pores, and diversities of preservation conditions under different structural styles and at different structural positions control different pore evolution stages. The shale gas in the mountainous complex structural area is characterized by horizontal zoning and differential enrichment. “Low thermal evolution rate and low maturity” and “slow structural uplifting” are beneficial to the long-term enrichment and preservation of shale gas. In conclusion, the mountainous complex structural area along the southwestern margin of the Sichuan Basin has a shale gas enrichment model of “sedimentation controlling source rocks, diagenesis controlling reservoirs and structure controlling preservation”. This research result provides idea and reference for searching for new shale gas areas and fields.