Distinguishing the differences of pore characters between different mixed lithofacies shales is helpful for improving shale gas development efficiencies. In this study, the targeted Longmaxi shale ( L1) of the Southern Sichuan Basin was selected as the research object. Two kinds of mixed lithofacies shale were identified by analyzing total organic carbon and X-ray diffraction results. The forming depositional environment of mixed lithofacies shale was researched by elements analyses. Pores in different mixed lithofacies shale were observed using field emission scanning electronic microscope. Low-field nuclear magnetic resonance and low-temperature nitrogen adsorption were conducted to analyze pore characters of different mixed lithofacies shale. The results showed that L1 were mainly composed of organic rich clay–siliceous mixed shales (OR-M-1) and organic extreme rich calcareous–siliceous mixed shales (OER-M-3). OR-M-1 and OER-M-3 were formed in high paleo-producing dysoxic–oxic seawater and anoxic waterbody, respectively. Micro-pore and meso-pore volumes of OER-M-3 were greater than those of OR-M-1 while macro-pore volume of OER-M-3 was lower than that of OR-M-1. Meso-pore surficial and structural complexities of OER-M-3 were greater than those of OR-M-1. OER-M-3 were greater in oil-wetting micro-pore structural complexities while lower in water-wetting micro-pore structural complexities, compared with OR-M-1. The inherent relationships between lithofacies type and sedimentary environment, total organic carbon, as well as pore characters, respectively, were quite close.