The determination of the Representative Elementary Volume (REV) is vital for comprehending the behavior of soil structural characteristics within the micro-to-macro framework. This study utilizes X-ray computed tomography to provide a detailed microscopic exploration of how waste cement, glass powder, and straw fibers contribute to the reduction of permeability in granite residual soils. Based on the pore reconstruction analysis of soil samples, the effect of REV size on the three-dimensional pore characteristics of modified granite residual soil is extensively studied. The results indicate that varying sizes of REV greatly affect the pore structure, porosity, fractal dimension, and permeability. Specifically, as the REV size increases, these parameters initially exhibit fluctuations characterized by uncertainty, ultimately stabilizing at a threshold value of 5000 μm. The incorporation of glass powder and straw fibers enhances the compactness of the soil while reducing the average diameter of connected pores. The alteration in the frequency distribution of connected pores redefines flow pathways, disrupting the preferential channels originally provided by larger pores, which is a primary factor that leads to the reduced permeability of the modified soil. These findings offer valuable references for determining the REV in modified soils, aiding future research in effectively saving time and computational costs.