Lacustrine shale oil resources offer a key opportunity for unconventional exploration, with accurate assessment of storage spaces in low to medium maturity shales being critical for resource development, energy security, and economic growth. This study examines Paleogene Kongdian Formation shales using petrological, geochemical, and quantitative pore size characterization methods to establish pore system models and identify key reservoir controls. Significant heterogeneity in porosity and pore size distribution is observed, with diameters ranging from 5 nm to 50 μm, predominantly within 5–200 nm. Shale pores exhibit complex networks dominated by irregular and slit-like shapes with varying connectivity. Five lithofacies display diverse pore types, with interparticle pores between feldspar, quartz, and carbonate minerals prevailing, though distribution varies significantly. Pore systems are primarily controlled by brittle mineral content, the development of laminations, and organic matter abundance. The findings suggests that OM-rich laminated siliceous and calcareous shales have high hydrocarbon generation potential, significant storage capacity, and a large proportion of brittle minerals, making them optimal targets for shale oil exploration in the region. This study also provides valuable insights into the relationship between lithofacies and shale storage capacity, advancing the understanding of reservoir mechanisms and hydrocarbon potential in lacustrine shales.