Quaternary mudstone biogas reservoirs in the Qaidam Basin have shown great potential. However, complex pore structures with high clay contents and high heterogeneity limit the understanding of the storage and migration principles of these reservoirs. In this paper, HPMI and nitrogen adsorption experiments, in combination with NMR experiments under water saturation, centrifugation, various drying temperatures and other conditions, were adopted to determine the pore structure characteristics. Specifically, the reservoir space types and pore radius distribution characteristics were clarified. The cutoff values for different types of pores were identified based on the water-saturated mudstone NMR T2 spectra for full aperture distribution scales jointly characterized by mercury injection and nitrogen adsorption experiments. Furthermore, the three pore components and the saturation of different fluids were obtained. The research results indicate that the mudstone biogas reservoir has developed various reservoir spaces, and the pore size is primarily in the micronanometer range. The average total porosity reaches 27.28%, but the proportion of movable water pores is only 9.23% with poor fluid mobility, and the fluids in the pores are mostly capillary-bound water and clay-bound water. Among the different lithologies, argillaceous sand is more likely to become a good production layer.