The classification of shale lithofacies, pore structure characteristics, and controlling factors of gas enrichment in deep-marine shale are critical for deep shale gas exploration and development. This study investigates the Late Ordovician Wufeng Formation (448–444 Ma) and Early Silurian Longyi1 submember (444–440 Ma) in the western Chongqing area, southern Sichuan Basin, China. Using experimental data from deep-marine shale samples, including total organic carbon (TOC) content analysis, X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), low-pressure N2 and CO2 adsorption, gas content measurement, and three-quartile statistical analysis, a lithofacies classification scheme for deep-marine shale was established. The differences between various global marine shale formations were compared, and the main controlling factors of gas enrichment and advantageous lithofacies for deep shale were identified. The results show that six main lithofacies were identified: organic-rich siliceous shale (S1), organic-rich mixed shale (M1), medium-organic siliceous shale (S2), medium-organic mixed shale (M2), organic-lean siliceous shale (S3), and organic-lean mixed shale (M3). Deep-marine shale gas mainly occurs in micropores, and the development degree of micropores determines the gas content. Micropore development is jointly controlled by the TOC content, felsic mineral content, and clay mineral content. TOC content directly controls the development degree of micropores, whereas the felsic and clay mineral contents control the preservation and destruction of micropores during deep burial. The large-scale productivity of siliceous organisms during the Late Ordovician Wufeng period to the Early Silurian Longmaxi period had an important influence on the formation of S1. By comparing the pore structure parameters and gas contents of different lithofacies, it is concluded that S1 should be the first choice for deep-marine shale gas exploration, followed by S2.