Structural deformation is one of the main impacts responsible for understanding the hydrocarbon accumulation mechanism. Predicting its function in gas storage and migration in a microscopic scale is thus a significant issue in predicting reservoir quality. The purpose of this article is to make a comparative study on the microstructure and petrophysical properties of undeformed and naturally deformed shales developed in the Southeast Sichuan Basin. The results show that (1) organic pores, ranging from 10 to 200 nm, are more developed in undeformed shale, whereas carbonate solvopores, clay-hosted pores, and microfractures are dominant in deformed shale. (2) Undeformed shales have Dubinin–Radushkevich (DR) CO2 adsorbed contents ranging between 0.009 and 0.018 g, DR CO2 micropore surface areas of 3.90–15.59 m2/g, and Dubinin–Astakhov (DA) CO2 micropore volumes of 0.002 and 0.035 cc/g. Naturally deformed shales have larger DR CO2 adsorbed contents, DR CO2 micropore surface areas, and DA CO2 micropore volumes, typically in the ranges of 0.019–0.031 g, 13.15–20.97 m2/g, and 0.006–0.012 cc/g, respectively. (3) Undeformed shales have N2 adsorbed contents ranging between 1.94 and 6.03 cc/g, Brunauer–Emmett–Teller (BET) N2 mesopore and macropore surface areas of 0.55–7.35 m2/g, and Barrett–Joyner–Halenda (BJH) N2 mesopore and macropore volumes of 0.002 and 0.006 cc/g. Naturally deformed shales have larger N2 adsorbed contents, BET N2 mesopore and macropore surface areas, and BJH N2 mesopore and macropore volumes, typically in the ranges of 5.72–14.45 cc/g, 7.47–17.64 m2/g, and 0.005–0.015 cc/g, respectively. (4) All samples have a unimodal micropore size distribution with a distinct peak associated with a 1.5 nm micropore fraction and have a multimodal mesopore and macropore size distribution. Naturally deformed shales show more homogeneous pore size distribution curves with morphological consistency than undeformed shales, indicating that structural deformation can significantly influence pore structural heterogeneity. (5) Deformed shales exhibit higher porosity and permeability compared to the undeformed samples due to the open pore-fracture network associated with the inorganic pores and microfractures. Average porosity and permeability in deformed shales can be 1.8 and 15 times higher than those in the undeformed shales. We conclude that the microstructural heterogeneity from strong to weak and the changes of a relatively single organic pore-dominated pore system to complex pores and microfractures dominated the pore-fracture system within shales due to structural deformation being the key cause of the quantitatively and qualitatively studied microstructure and petrophysical property differences.