Abstract: The Ordovician-Silurian Wufeng and Longmaxi Shale in the Sichuan Basin were studied to understand the genesis and diagenetic evolution of carbonate minerals and their effects on reservoir quality. The results of geochemical and petrological analyses show that calcite grains have a negative Ce anomaly indicating they formed in the oxidizing environment of seawater. The high carbonate mineral contents in the margin of basin indicate that calcite grains and cores of dolomite grains appear largely to be of detrital origin. The rhombic rims of dolomite grains and dolomite concretions with the δ13C of –15.46‰ and the enrichment of middle rare earth elements were formed during the sulfate-driven anaerobic oxidation of methane. The calcite in radiolarian were related to the microbial sulfate reduction for the abundant anhedral pyrites and δ13C value of –11.34‰. Calcite veins precipitated in the deep burial stage with homogenization temperature of the inclusions ranging from 146.70 °C to 182.90 °C. The pores in shale are mainly organic matter pores with pore size mainly in the range of 1–20 nm in diameter. Carbonate minerals influence the development of pores through offering storage space for organic matter. When calcite contents ranging from 10% to 20%, calcite grains and cement as rigid framework can preserve primary pores. Subsequently, the thermal cracking of liquid petroleum in primary pores will form organic matter pores. The radiolarian were mostly partially filled with calcite, which combining with microcrystalline quartz preserved a high storage capacity.