The Cenozoic continental strata of the Bohai Bay Basin are rich in shale oil resources, and they contain various types of reservoir spaces that are controlled by complex factors. Using field emission scanning electron microscopy (FE-SEM), automatic mineral identification and characterization system (AMICS), CO2 and N2 gas adsorption, and focused ion beam scanning electron microscopy (FIB-SEM), the types of shale reservoir spaces in the Bohai Bay Basin are summarized, the spatial distribution and connectivity of the various types of pores are described in detail, the microscopic pore structures are characterized, and the key geological mechanisms affecting the formation and evolution of the reservoir spaces are determined. Three conclusions can be drawn in the present study. First, the shale reservoir spaces in the Bohai Bay Basin can be divided into three broad categories, including mineral matrix pores, organic matter pores, and micro fractures. Those spaces can be subdivided into seven categories and fourteen sub-categories based on the distribution and formation mechanisms of the pores. Second, the complex pore-throat structures of the shale reservoir can be divided into two types based on the shape of the adsorption hysteresis loop. The pore structures mainly include wedge-shaped, flat slit-shaped, and ink bottle-shaped pores. The mesopores and micropores are the main contributors to pore volume and specific surface area, respectively. The macropores provide a portion of the pore volume, but they do not significantly contribute to the specific surface area. Third, the factors controlling the development of microscopic pores in the shale are complex. The sedimentary environment determines the composition and structure of the shale and provides the material basis for pore development. Diagenesis controls the types and characteristics of the pores. In addition, the thermal evolution of the organic matter is closely related to inorganic diagenesis and drives the formation and evolution of the pores.