Physical soil crusts will form on most soils during and after rainfall and it has important effects on the runoff and sediment on slopes. However, objective and effective methods for quantifying the characteristics of physical soil crusts (such as the thickness) are not currently available. We used a new method for determining the thickness of physical soil crusts based on X-ray computed tomography (CT) in order to quantify the thickness of the structural crust (SC) and depositional crust (DC) for two typical erosive soils comprising granite red soil (GRS) and Quaternary red clay (QRC) in the red soil region of southern China. The pores in the GRS and QRC were characterized as finely and densely spatially distributed, with an average porosity of 15.47% and a range of 1.66–28.83%. The soil porosity increased rapidly in the 0–3 mm depth, but the porosity of the SC and DC soil samples generally decreased or was stable in the 3–30 mm depth. The average thickness of the soil crust was 1.31 mm, and the average thicknesses of SC and DC were 1.16 and 1.46 mm, respectively. The thickness of SC of GRS decreased with the slope, whereas the thickness of DC of QRC generally increased with the slope. The thickness of SC increased with runoff yield and its contribution rate to the runoff cannot be neglected. The study provides a method for the objective quantification of physical soil crust and can deepen the research on slope erosion process and influencing factors.