The hydrothermal dolomitization, facilitated by basement fault activities, had an important impact on the Permian Maokou Formation dolomite in the Sichuan Basin, which experienced complex diagenesis and presented strong reservoir heterogeneity. The source and age of diagenetic fluids in this succession remain controversial. In this study, various analyses were implemented on samples collected from outcrops and wells near the No. 15 fault in the eastern Sichuan Basin to reconstruct the multi-stage fluid activity and analyze the impact on reservoir development, including petrology, micro-domain isotopes, rare earth elements, homogenization temperature of fluid inclusions, and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) U-Pb dating. The homogenization temperature of primary brine inclusions in fine-grained matrix dolomite and saddle dolomite is concentrated between 100 and 150 °C, which indicates that the impacts of abnormally high temperatures of other geological bodies. The δ13C and δ18O value and low 87Sr/86Sr value indicate that the diagenetic fluid of fine-grained matrix dolomite is mainly Permian seawater. The U-Pb ages of fine-grained matrix dolomite are ~260 Ma, which coincides with the age of the main magmatism of Emeishan Large Igneous Province (ELIP), and hydrothermal fluid provided a favorable high-temperature environment in the penecontemporaneous stage. While highly radiogenic 87Sr/86Sr compositions suggests those of saddle dolomite, the high-temperature Sr-rich formation fluid. The U-Pb ages of saddle dolomite are 245–250 Ma, which coincides with the age of the 255~251 Ma magmatism of ELIP. This indicates that those should be the diagenetic products of the ELIP hydrothermal fluid in the shallow burial stage. The U-Pb age of coarse-grained calcite is 190–220 Ma, and it should be the diagenetic product of the deep burial stage. Brine inclusions associated with primary methane inclusions were developed in coarse-grained calcite, with a homogenization temperature range of 140.8–199.8 °C, which indicates that the formation fluid activities were related to hydrocarbon charging. The Permian Maokou Formation dolomite was firstly formed in the penecontemporaneous shallow burial stage, and then it was subjected to further hydrothermal dolomitization due to the basement faulting and the abnormally high heat flow during the active period of ELIP. Hydrothermal dolomitization contributed to the formation and maintenance of intercrystalline and dissolution pores, whereas it also formed saddle dolomite to fill the pores, and reduce the pore space. The influence of deep fluid activities on reservoir evolution is further distinguished.