The research of microscopic pore structure characteristics is the core issue of shale gas reservoir，and the summary of influencing factor is mainly based on single factor analysis. The causes and differences of different types of shale gas reservoir and its microscopic pore structure were summarized from the aspects of petrology，sedimentology and organic geochemistry. The result shows that shales formed in different sedimentary environments have very different microscopic pore structure after a series of diagenetic and thermal evolution. The sedimentary environment determines the content of TOC，brittle minerals and clay minerals in shale，which is the material foundation for the formation of microscopic pores. The types and development degree of microscopic pore structure vary with diagenetic evolution stages of shale. The influence of thermal evolution on microscopic pores shows that a large amount of organic matter pores occur with the increase of maturity and the specific surface area and pore volume will change with the transformation of clay minerals. Based on multi-factor analysis，three-element coupled control on microscopic pore structure was proposed including sedimentary environment，diagenetic evolution and thermal evolution，and the mainly controlling elements at different evolution stages were also analyzed.