The pore-fracture network within shale significantly controls the microscopic storage of hydrocarbons. The Paleogene lacustrine Shahejie Formation of Bohai Bay Basin represents an outstanding lower-thermal-maturity example of a mineral matrix pore-fracture system. Recent studies have shown that most pores in Shahejie shale detectable by high-resolution electron microscopy are associated with an inorganic mineral matrix instead of organics. However, because of the lack of both qualitative and quantitative data on nanometer to micrometer scales, such microstructures have limited the ability to predict hydrocarbon storage feature. Representative Shahejie shale samples come from the Well F39X1 to investigate the pore-fracture network using a synergistic multiscale multi-dimensional workflow by field emission scanning electron microscopy, multi-scale CT, and FIBSEM. Investigations in both 2D and 3D and across cm−mm−μm−nm length scales indicate heterogeneity at every scale and dimensions. From 2D SEM images, clay flake-hosted interparticle pores, rigid grain-hosted interparticle pores, intraparticle dissolution pores, grain-rim microfractures, intragranular microfractures, and matrix microfractures are identified with varying numbers, sizes, and geometries. Large field-of-view 2D scanning electron microscopy images were also used to quantitatively and statistically study the abundance and size of pores and fractures. Using multi-scale CT techniques, pores and fractures from centimeter to nanometer scales were observed with preferential propagation along the mineral aggregate-rich laminations, resulting in an interconnected pore-fracture network. Using FIBSEM, the mineral/organic particles and their related pore phases were visualized, quantitatively computing the pore size and abundance. The visual results suggest that the mineral matrix pore-fracture network in lacustrine Shahejie Formation plays a key role as the liquid hydrocarbon storage space. The application of these techniques to the lower-thermal-maturity shale reservoirs provides important insights into estimating and visualizing rock microstructural heterogeneity and preliminarily establishing a liquid hydrocarbon microscopic storage model.