Currently, more attention has been given to the study of the microstructure of contaminated clay, while few studies have focused on the analysis of SEM images of clay from a threshold perspective. The purpose of this paper was to determine the threshold range of image pixel values for municipal waste-contaminated clay by observing and processing SEM images of municipal waste-contaminated clay under different seepage depths and concentrations. In this study, municipal waste-contaminated clay samples were obtained at different depths in a column test exhibiting different CaCO3 and CH3COOH concentrations, imaged through SEM and subjected to binarization. Three steps for determining the pixel threshold value of the SEM images were described, including preprocessing and binarizing the SEM images in Image Pro Plus 6.0 (IPP) and morphological processing by the Pores (Particles) and Cracks Analysis System V2.3 (PCAS). The apparent void ratio of contaminated clay and the fractal dimension of clay particles were applied as evaluation parameters. The determined effective threshold range of the image pixel values of municipal waste-contaminated clay was 110–140. The accuracy of this method was verified in three aspects: the relationship between the threshold value and the apparent void ratio, the variation in pore blockage with seepage depth, and the characteristics of the compaction factor with seepage depth and pollutant concentration.