Global recoverable shale gas reserves are estimated to be 214.5 × 1012 m3. Estimation methods for shale gas resources, such as volumetric, analog, and genetic approaches, have been widely used in previous studies. However, these approaches have notable limitations, including the substantial effect of rock heterogeneity, difficulties in determining the similarity of analog accumulations, and unsuitability for evaluating high-mature–overmature source rocks. In the Qiongzhusi Formation (Є1q) of the Sichuan Basin, China, extensive development of high-mature–overmature shales has led to significant advancements in conventional and unconventional shale gas exploration. This progress highlights the need for the development of an integrated evaluation system for conventional and unconventional resources. Hence, this study uses the whole petroleum system theory and an improved hydrocarbon generation potential method to analyze the distribution patterns of hydrocarbon generation, retention, and expulsion during various stages of oil and gas accumulation in the Є1q. In addition, it assesses the resource potential of conventional and shale oil and gas. Hydrocarbon generation and expulsion centers are favorable exploration targets for conventional oil and gas, primarily located in the central and northern regions of the Mianyang—Changning rift trough, with an estimated resource potential of 6560 × 1012 m3. Hydrocarbon retention centers represent promising targets for shale oil and gas exploration, concentrated in the central Mianyang—Changning rift trough, with a resource potential of 287 × 1012 m3. This study provides strategic guidance for future oil and gas exploration in the Є1q and offers a methodological reference for integrated resource assessments of conventional and unconventional oil and gas systems of high-mature–overmature source rocks in similar basins worldwide.