<p>Ultra-deep carbonate oil and gas resources represent a key frontier for future oil and gas exploration and development. Complex fluid activities exert a significant influence on the diagenesis, reservoir formation, and hydrocarbon accumulation processes in ultra-deep carbonate rocks. In the Middle Permian Maokou Formation of the northern Sichuan region, a variety of minerals, predominantly calcite, extensively fill the pores and fractures, yet their origins and the associated fluid evolution processes remain unclear. To address this issue, this study employs petrographic analysis, C-O-Sr isotope characterization, rare earth element (REE) geochemistry, fluid inclusion analysis, and U-Pb geochronology, in conjunction with the burial-thermal evolutionary history. The research focuses on calcite cements occurring in the pores and fractures of the Maokou Formation, aiming to clarify their genesis in the Yuanba area and evaluate their significance for hydrocarbon exploration. The results indicate that the lithology of the Maokou Formation is predominantly composed of bioclastic limestone, bioclastic micritic limestone, and micritic bioclastic limestone. Pores and fractures within the formation are filled with three successive stages of calcite cements: mud-powder crystal calcite (Cal-1) → fine-medium crystal calcite (Cal-2) → coarse crystal calcite (Cal-3). The δ¹³C, δ¹⁸O, and ⁸⁷Sr/⁸⁶Sr values of the first-stage cements are comparable to coeval seawater values. The mixing of seawater and meteoric water in the pore space results in increased concentrations of Ca²⁺ and CO₃^2-, promoting precipitation. Cal-1 formed in the Late Permian–Early Triassic, in response to changes in temperature and pressure due to increased burial depth. The δ¹⁸O values of the second-stage cements exhibit a negative shift. Dissolution of Maokou Formation carbonates released Sr²⁺ and Ca²⁺ into the formation water, thereby increasing ⁸⁷Sr/⁸⁶Sr ratios and returning Ca²⁺ concentrations to saturation. As temperature and pressure changed with continued burial, Cal-2 precipitated during the Late Triassic–Early Jurassic, as constrained by a U–Pb age of 214.2 ± 4.8&#xa0;Ma. The third-stage cement is characterized by low δ¹³C and δ¹⁸O values, elevated ⁸⁷Sr/⁸⁶Sr ratios, and a pronounced positive Eu anomaly in the REE pattern. Deep hydrothermal fluids carrying substantial concentrations of Ca²⁺ and CO₃^2- migrated along structural fractures into the Maokou Formation. As temperature and pressure decreased, Cal-3 condensed and precipitated, forming during the Middle Jurassic. Based on the type and abundance of hydrocarbon inclusions in calcite cements, a correlation between reservoir densification and hydrocarbon charging was established. It was determined that densification before hydrocarbon charging is the primary factor contributing to the limited natural gas accumulation in the Maokou Formation of the Yuanba area. <i>The findings suggest that for deep limestone reservoirs lacking or weak dolomitization</i>,<i> early hydrocarbon charging plays a critical role in preserving reservoir quality</i>,<i> ultimately controlling the extent of hydrocarbon enrichment.</i></p>