The 2nd member of the Paleogene Kongdian Formation (Kong 2 Member) in the Cangdong Sag, Bohai Bay Basin contains thick-bedded organic-rich shale sequences, suggesting promising prospects for resource exploration. However, there remains a lack of a systematic understanding of the coupling relationships between the lithofacies and pore structure of shales, restricting the thorough analysis of shale oil enrichment mechanisms. This study aims to determine the microscopic pore structure characteristics of reservoirs of different lithofacies in the Kong 2 Member shales within the Cangdong Sag. Specifically, the microscopic pore structures are characterized at multiple scales using a range of techniques, including X-ray diffraction (XRD), total organic carbon content (TOC) analysis, argon ion milling-field emission scanning electron microscopy (FE-SEM), N₂ and CO₂ adsorption, the automated mineral identification and characterization system (AMICS), and three-dimensional (3D) reconstruction using focused ion beam-scanning electron microscopy (FIB-SEM). The results reveal that five shale lithofacies occur in the study area: lamellar felsic shale, lamellar mixed shale, massive mixed shale, lamellar carbonate shale, and massive carbonate shale. These shale lithofacies contain various types of reservoir spaces, including inorganic pores, organic pores, and microfractures, with significant variations in pore structure. Nevertheless, in all shale lithofacies, the pore sizes predominantly range from 2 nm to 200 nm, with nanopores acting as the primary contributors to the reservoir space. Among these lithofacies, the lamellar felsic shale and lamellar mixed shale exhibit large pore volumes due to the presence of macro-pores and microfractures. In contrast, the organic-rich lamellar shale exhibits higher connectivity compared to other lithofacies. Regarding the occurrence states of organic matter, syngenetic organic matter, interstitial organic matter, and organic matter-clay mineral complexes exhibit diverse morphologies and contact relationships with surrounding minerals, contributing differently to pore volume and connectivity. Notably, the syngenetic organic matter in high-frequency lamellar shale can improve the pore structure. The deposition and evolution of organic matter and mineral components control the modification of reservoir pore systems. The compressive resistance of the felsic mineral matrix is favorable for pore preservation. In contrast, although lamellar and massive carbonate shales contain extensively developed dissolution pores, the cementation between minerals limits their porosity and connectivity. Furthermore, erosional fluids generated under moderately high TOC content and thermal evolution migrate along lamina interfaces and microfractures, playing a significant role in creating differential reservoir performance across the various shale lithofacies.