The characterization of pore systems in fine-grained carbonate rocks faces numerous challenges due to the significant complexity of microscopic features, including a variation of micro- and nanoscale pore sizes and the complex pore-throat distribution. In this work, digital core technology was adopted to characterize the pore systems of lacustrine fine-grained carbonate rocks in the Yingxi area of Qaidam Basin. The simulated results indicated that the pore types predominantly contain intercrystalline and dissolution pores. The former exhibit high porosity but extremely low permeability and are primarily developed in bedded dolostones. Conversely, the latter show relatively higher permeability, predominantly developed in bedded calcareous dolostones. The elevated dolomite content provides the material basis for the development of intercrystalline pores, while the extremely small throat radius constrains the fluidity of this pore system. In addition, the dissolution has a great impact on improving the permeable capability of intercrystalline pore system via increasing the radius and specific surface area of pores and throats.