The formation and distribution of carbonate minerals have important influences on reservoir development. The dissolution-precipitation effect plays an important role in controlling the reformation of reservoir physical properties. High-quality source rocks with abundant reserves exist in the Lower Permian Fengcheng Formation, Junggar Basin, China, and the basin reservoir contains a large amount of carbonate minerals. Multi-stage cementation and dissolution of these carbonate minerals have important influences on diagenesis-porosity evolution of the reservoirs. Because of the coupled influences of deep fluid transformation and volcanic activity in the diagenetic evolution of the Fengcheng Formation, it has experienced a complex evolution of carbonate minerals. In this study, through core observation, thin section, X-ray diffraction mineral composition, carbon and oxygen isotope, fluid inclusion homogenization temperature, and laser Raman and cathodoluminescence analysis, the material sources, development period, dissolution-precipitation reactions, and transformation mechanisms of carbonate minerals in the diagenetic evolution of the Fengcheng Formation reservoir were evaluated in detail. Finally, the controlling effect of multi-stage cementation of carbonate minerals on the reservoir physical properties was determined. The results showed that there are three stages of carbonate minerals in the Fengcheng Formation. The material source of the early carbonate was mainly terrigenous debris, and the formation temperature range was 30–70 °C. The material source of middle-late carbonate minerals was mainly decarboxylation of organic acid, and the formation temperature was 60–110 °C. In addition, some were generated through hydrothermal metasomatism at high ambient temperatures, up to 120 °C. In areas where early carbonate minerals are well developed, a large number of microcracks was more likely to form under the influence of tectonic movements, resulting in high-quality reservoirs. The formation of late carbonate minerals, which is the main reason for reservoir densification in the later stage of diagenesis, resulted in poor reservoir physical properties. This study provides information useful for predicting the distribution areas of favorable reservoirs in the Fengcheng Formation, and a theoretical basis and guidance for improving the accuracy of shale oil exploration and development.