Enhancing the sealing capacity of temporary plugging layers is essential for achieving successful diversion fracturing. The permeability of these layers is determined by their internal pore structure, which evolves under mechanical compression during formation closure. In this study, micro-computed tomography (Micro-CT) was utilized to establish a quantitative method for characterizing the three-dimensional pore geometry of temporary plugging layers composed of resin-based particles. Structural parameters including porosity, pore radius, throat radius, and tortuosity were analyzed under multiple compaction conditions, and the corresponding permeability was experimentally measured. Results indicate that increased compaction produces denser particle packing, leading to reductions in porosity, pore–throat dimensions, and overall permeability, while tortuosity increases continuously. Based on these relationships, a predictive model coupling compaction behavior and particle filling effects was developed to describe the permeability evolution under stress. The proposed model provides practical guidance for selecting and blending temporary plugging materials in field fracturing applications.