Abstract: The biogas of Quaternary weak diagenetic shale has a wide exploration prospect, and the understanding of pore structure and physical properties of these shales is conducive to promote the geological theory of shale biogas reservoir. The Quaternary weak diagenetic shale from the Sanhu area of Qaidam Basin was employed as an example in this study, to study the pore structure and physical properties by the means of scanning electron microscopy, thin section observation, X-ray diffraction of whole-rock samples, overpressure pore permeability determination, relative permeability of gas-water etc. Results show that there are three types of lithofacies for the Quaternary weak diagenetic shales including clay shales, mixed shales and felsic shales, and pores appeared to include intergranular pores, inner pores of brittle mineral grains, inner pores of clay mineral grains and organic pores. The pore size of felsic shale is large, mainly micron pores. The pore size of clay shale and mixed shale are dominated by nano-scale pores. The peak porosity and permeability of Quaternary weak diagenetic shale distribute in the range of 15%-30% and (0.1-10) ×10^-3 μm², respectively, and significantly reduce under overburden conditions. The residual water saturation after displacement is high (with an average value of 58.7%). Due to clay expansion, the effective pore space is reduced and the fluidity of gas and water is restrained, resulting in very low relative permeability of gas and water in the two-phase co-flow zone.