The Permian Fengcheng Formation in the Mahu Sag of the Junggar Basin is characterized by frequent changes of mineral compositions and lamina structure. The alkali lacustrine shale reservoir shows strong heterogeneity and anisotropy, it is particularly important to clarify the relationship between pore structure and reservoir quality. The pore characteristics were investigated by using thin sections, Scanning Electron Microscope (SEM), and Nuclear Magnetic Resonance (NMR) analyses. The pore types are mainly composed of inorganic pores, organic pores, and microfractures. The storage space is dominated by inorganic pores and microfractures. The pore structure was divided into four types by NMR parameters including T2 spectral morphology, T2gm, total porosity, and movable fluid porosity. Combined with core NMR experiments and two-dimensional (2D) NMR logs, 21 ms was adopted as the T2cutoff value to represent the demarcation between movable and bound fluids. From Type I to Type IV, the energy clusters reflect the movable fluids including movable oil and movable water gradually decreasing in the upper right corner. The energy clusters reflect the bound fluids including clay-bound water and bitumen gradually increasing in the lower left corner in the T1-T2 map. The results show that the heterogeneity of mineral compositions and lamina structures are the key factors directly leading to the complexity and distribution of pore structure. Quartz with strong compaction resistance helps keep a large number of primary interparticle pores, and feldspar dissolution pores caused by organic acids are present. Dolomite intercrystalline pores and dissolution pores provide a large amount of storage space for the shale, while the cementation of calcite reduces pore spaces. The increase of felsic mineral content is conducive to improving the pore structure and oil-bearing potential of oil shale reservoir, while clay minerals and calcite are contrary. There are abundant primary interparticle pores and dissolution pores in the layered siliceous (felsic) shales, and they consist of the upper sweet spot in the Fengcheng Formation. The longitudinal time (T1) and transverse time (T2) spectra are bimodal with high total porosity and movable oil content, reflecting high reservoir quality and oil-bearing property. Laminated dolomite shales contain dolomite intercrystalline pores and dissolution pores, and they consist of the lower sweet spot in the Fengcheng Formation. The results above provide a new perspective on the evaluation of pore structure and reservoir quality of shales in the context of an alkaline lake.