Shale with a maturity within the “oil window” contains a certain amount of residual soluble organic matter (SOM). This SOM have an important influence on characterization of shale reservoir. In this study, two shale samples were collected from the Upper Permian Dalong Formation in the northwestern boundary of Sichuan Basin. Their geochemistry, mineral composition, and pore structure (surface area and pore volume) were investigated before and after removing the SOM by means of extraction via dichloromethane or trichloromethane. The results show that the TOC, S1, S2, and IH of the extracted samples decrease significantly, but the mineral composition has no evident change as compared with their raw samples. Thus, we can infer that the original pore structure is thought to be unaffected from the extraction. The SOM occupies pore volume and hinders pores connectivity. The extraction greatly increases the surface area and pore volume of the samples. The residual SOM in the shale samples occur mainly in the micropores and smaller mesopores, and their occupied pore size range seems being constrained by the maturity. For the lower mature shale samples, the SOM is mainly hosted in organic pores that are less than 5 nm in size. For the middle mature shale samples, the micropores and some mesopores ranging between 2 and 20 nm in size are the main storage space for the SOM.