Accurate quantification of moisture content redistribution and physical property change due to freeze–thaw is important for understanding frost heave and thaw settlement of fine-grained soils including clay. This paper presents 3D X-ray Computed Tomography (CT) data for a clay specimen before and after freeze–thaw and physical property data obtained by conventional laboratory testing, and the relationship among the date sets. Undisturbed clay specimens were subject to one-directional freeze–thaw in a closed system under different freezing temperatures to collect 3D X-ray CT images, and the variation in CT image intensity (CTI) before and after freeze–thaw were analyzed to reveal the spatial effects of freeze–thaw. Meanwhile, soil properties including moisture content, void ratio, and dry density were obtained for samples taken from different heights of the specimens with and without freeze–thaw to obtain their changes. Close correlations were observed between the physical property changes and the CTI variation. Linear equations were established between the changes of physical properties and the CTI variation. These equations could potentially be applied for high-resolution quantitative assessment of soil physical property changes due to freeze–thaw by using 3D X-ray CT. This study demonstrates that, compared with traditional test methods, CT scanning can be advantageous in revealing the internal change in soil physical properties due to freeze–thaw quantitatively and nondestructively.