To optimize the dry mixing preparation process for permeable asphalt mixtures and elucidate the microscopic mechanism of high-viscosity modifiers, this study employed Response Surface Methodology (RSM). Independent variables, including mixing temperature, dry mixing time, and wet mixing time, were selected, with Marshall stability, −10 °C splitting tensile strength, and residual stability as response indicators. The significance and fitting accuracy of the model were evaluated through Analysis of Variance and residual diagnosis. Additionally, the morphological evolution, spatial distribution, and chemical interactions of the modifier were characterized using scanning electron microscopy (SEM), fluorescence microscopy (FM), and Fourier Transform Infrared Spectroscopy (FTIR). The results revealed distinct differences in factor effects: mixing temperature most strongly influenced high-temperature performance, while wet-mixing time primarily governed low-temperature performance and water stability. Furthermore, significant interactions were observed among the variables. Multi-objective optimization determined the optimal process parameters to be a mixing temperature of 182 °C, dry mixing time of 180 s, and wet mixing time of 102 s. Experimental validation confirmed that the relative error between predicted and actual values was within 5%. Microscopic characterization revealed that under the dry mixing process, the modifier undergoes four stages: rapid melting, viscous flow, permeation diffusion, and swelling development. An appropriate mixing temperature combined with sufficient dry and wet mixing times promotes the formation of a uniform, dense spatial network structure of the modifier within the asphalt. This study validated the reliability of RSM in process optimization, providing theoretical foundations and key technical parameters for the green and efficient production of high-performance permeable asphalt mixtures.