Under high-temperature and high-pressure condition, accurate characterization of the pore throat size distribution and its intrinsic correlation with drilling fluid intrusion damage remains challenging due to the complexity and heterogeneity of the reservoir’s microscopic pore structure. In this research, a high-temperature high-pressure dynamic fluid loss experimental device, independently developed by Southwest Petroleum University, was adopted. This device shows significant improvements in temperature resistance, pressure resistance, and the stability of the circulation system. Based on this device, the dynamic fluid loss process of drilling fluid was optimized. Permeability damage evaluation experiments were conducted, along with multi-scale characterization techniques such as casting thin sections and scanning electron microscopy. The distribution characteristics of typical pores, mainly intergranular pores, feldspar dissolution pores, and kaolinite intergranular pores were analyzed. The pore throat structure characteristics in permeable rock samples and the permeability evolution law during drilling fluid intrusion were investigated. Differentiated responses of various pore morphologies to the solid-phase invasion of drilling fluid were revealed. Experimental results indicate that the fluid loss dynamics curve of medium- and high-porosity permeable rock samples shows a slowly decreasing trend, with a relatively long stable stage. In contrast, low-porosity and low-permeability samples exhibit rapid filtration loss attenuation, and the duration of the stable stage is relatively shorter. Observations from cast thin sections, scanning electron microscopy, and energy spectrum analysis show that contamination is relatively severe in intergranular pores and feldspar dissolution pores, while it is weaker in kaolinite intergranular pores. Moreover, the invasion and deposition of solid particles and chemical substances from the drilling fluid into the reservoir pores are identified as the main reasons for the decrease in reservoir permeability. The degree of pollution is closely related to the pore size. By establishing a quantitative relationship model between borehole throat structure parameters and the degree of drilling fluid damage, this study provides a theoretical basis for optimizing reservoir protection schemes and enhancing oil and gas recovery rates.