Identifying the origin, evolution and distribution of overpressure poses a significant challenge in shale gas reservoir, particularly in the deeper layers and zones of the Wufeng-Longmaxi Formations. To uncover the origin mechanism and reconstruct the evolution process of overpressure, samples are collected from the Wufeng-Longmaxi Formations in the southern Sichuan Basin. Subsequently, a combination of multi well-logging methods is employed to comprehensively identify the origin mechanism of overpressure. Additionally, forward numerical simulation and Laser Raman inversion validation are utilized to reconstruct the evolution process of overpressure during burial. Results show that: (1) Hydrocarbon generation pressurization is identified as the dominant origin mechanism of overpressure in the Wufeng-Longmaxi shale gas reservoir, employing a combination of well-logging methods, the revised Bowers method, and a velocity-density intersection chart. (2) The Wufeng-Longmaxi shale undergoes three main pressurization processes, including kerogen generation oil pressurization, crude oil cracking gas pressurization and kerogen cracking gas pressurization. Hydrocarbon generation pressurization correlates closely with factors such as organic matter abundance and type, original hydrogen index, kerogen mass fraction and transformation rate, oil cracking rate and retention coefficient. (3) The pressure coefficient of kerogen generation oil pressurization and gas cracking pressurization reaches 1.73 and 2.78, respectively. The contribution of crude oil cracking gas pressurization (75.6 MPa) is significantly greater than kerogen generation oil pressurization (37.8 MPa). (4) The density of methane inclusions (0.290–0.319 g/cm3) is corroborated through both Laser Raman spectroscopy and homogenization temperature analysis. The paleo pressure is recovered as 90.3–193.5 MPa, with a corresponding pressure coefficient spanning from 1.39 to 2.98. This study not only contributes to the advancement of the shale gas accumulation theory, but also provides valuable insights to guide the further exploration and development of marine shale gas within the intricate tectonic setting of the Sichuan Basin.