Many factors need to be considered in the evaluation of tight conglomerate reservoirs, including the microscopic pore-throat structure, pore connectivity, lithology, porosity, permeability, and clay mineral content. The contents and types of clay minerals reflect the mineral evolution process during the deposition of the reservoir and can reflect the reservoir’s physical properties to a certain extent. In this study, cores from the Baikouquan Formation in Mahu were used to comprehensively analyze the effects of the clay mineral content on the physical properties of a tight conglomerate reservoir, including field emission scanning electron microscopy (FE-SEM), casting thin section observations, X-ray diffraction (XRD), interface property testing, high-pressure mercury injection, low temperature N2 adsorption, and nuclear magnetic resonance (NMR)-movable fluid saturation testing. The results revealed that differences in different lithologies lead to differences in clay mineral content and pore structure, which in turn lead to differences in porosity and permeability. The interface electrification, adsorption, and specific surface area of the reservoir are positively correlated with the clay mineral content, which is mainly affected by the smectite content. As the clay mineral content increases, the proportion of nanoscale pore throats increases, and the core becomes denser. The saturation of the movable fluid controlled by the >50 nm pore throats in the .tight conglomerate ranges from 8.7% to 33.72%, with an average of 20.24%. The clay mineral content, especially the I/S (mixed layer of Illite and montmorillonite) content, is negatively correlated with the movable fluid. In general, the research results clarified the relationship between the lithology and physical properties of clay minerals and the microscopic pore structure of the tight conglomerate reservoirs in the Baikouquan Formation in the Mahu area.