Abstract: Eastern Sichuan Basin is a critical region for oil and gas production in China, and the thermal effect of the Emeishan Mantle Plume (EMP) on the basin remains unclear, which limits the study of the Paleozoic hydrocarbon accumulation process. Thus, clarifying the thermal history is crucial for oil and gas evaluation and exploration. This study combines zircon fission track (ZFT), zircon (U-Th)/He (ZHe), and vitrinite reflectance analyses to reconstruct the thermal history since the Paleozoic and investigate the maturity evolution of Paleozoic source rocks in the eastern Sichuan Basin. Additionally, the contributing factors of the Permian abnormal heat flow and the thermal effect range of the EMP were analyzed. Thermal history results show a stable low heat flow phase (45–55 mW/m2) from the Cambrian to Permian, a rapid increase to peak values (62–70 mW/m2) during the Middle Permian, and a gradual decline to current stable values (47–62 mW/m2) from the Triassic onward. Thermal evolution revealed that Paleozoic source rocks exhibited maturation stagnation due to tectonic events, while the Permian peak heat flow and the Jurassic-Late Cretaceous rapid burial accelerated maturation. The Cambrian Qiongzhusi Formation and Silurian Longmaxi Formation source rocks began generating hydrocarbons (Requ = 0.5%) in the Late Cambrian–Late Ordovician and Late Silurian–Early Devonian, respectively, while it was Late Permian–Early Triassic for Permian source rocks. Peak maturity (Requ > 2%) occurred in the Late Cretaceous, with natural gas as the dominant product. The EMP significantly influenced the thermal regime of the western and central Sichuan Basin, with a thermal effect radius of ∼600–650 km. In contrast, the Permian thermal anomaly in the eastern Sichuan Basin is attributed to the lithospheric extension associated with the Middle Permian Kaijiang-Liangping trough. These findings provide critical insights for deep and ultra-deep gas exploration and enhance the understanding of the EMP's regional thermal impacts.