Based on backscattered electron (BSE) images, the performances of the frequency-grayscale histogram, cumulative frequency-grayscale histogram, and Gaussian mixture model methods in phase analysis of cement-based repair materials were compared, and the phase proportions in the repaired interfacial transition zones were studied based on the optimal method. The results indicate that the Gaussian mixture model method exhibits the best stability and consistency, and it is recommended for use in grayscale threshold segmentation for quantitative phase analysis. Additionally, it is found that pores and unreacted particles are densely distributed in repaired interfacial transition zones, with a higher content of unreacted particles in modified Portland cement-based repair materials and a greater proportion of pores in phosphate cement-based repair materials, so the appropriate treatment should be applied in repair work to enhance the effectiveness of the repair.