Various types of pores, including organic and inorganic variations, exhibit distinct impacts on the storage capacity of shale gas reservoirs and play a significant role in shale gas occurrence. However, there is a limited number of studies that have quantitatively addressed the developmental characteristics of these diverse pore types and their primary controlling factors. This paper explores the development of inorganic pores, specifically interparticle pores and intraparticle pores, as well as organic matter (OM) pores within the shales of the Wufeng–Longmaxi Formation in the Upper Yangtze region. Parameters such as areal porosity, pore diameter, and pore number based on the FE-SEM and image digitization are discussed. Additionally, the influence of the sedimentary environment on the development of various pore types through integrated wavelet transform techniques and geochemical analysis are analyzed. This analysis reveals the distinctive mechanisms governing the development of pore types under the sequence stratigraphic constraints. The findings reveal that the Wufeng–Longmaxi Formation within the study area can be classified into four systems tracts (transgressive systems tracts TST1 and TST2, and highstand systems tracts HST1 and HST2). Within TST1+HST1, OM pores emerge as the predominant pore type, contributing to over 65% of the porosity. TST2 similarly displays OM pores as the dominant type, comprising over 45% of the total porosity, with an average OM areal porosity of 7.3%, notably lower than that of TST1+HST1 (12.7%). Differences in OM pore development between TST1+HST1 and TST2 shales are attributed to variations in OM abundance and type. In HST2, inorganic pores are the dominant pore type, primarily consisting of interparticle pores associated with clay minerals, contributing to more than 50% of the porosity, while OM pores remain almost undeveloped. The frequent sea level fluctuations during the sequence stratigraphic evolution caused variations in sedimentary environments across different depositional sequences. These differing depositional environments lead to varying OM content and types, mineral genesis, and content, ultimately resulting in disparities in the development of shale pore types within different sequences.