Soil chemical washing has the disadvantages of long reaction time, slow reaction rate and unstable effect. Thus, there is an urgent need to find a cost-effective and widely applicable alternative power to facilitate the migration of washing solutions in the soil, so as to achieve efficient removal of heavy metals, reduce the risk of soil compaction, and mitigate the damage of soil structure. Therefore, the study used a combination of freeze-thaw cycle (FTC) and chemical washing to obtain three-dimensional images of soil pore structure using micro-X-ray microtomography, and applied image analysis techniques to study the effects of freeze-thaw washing on the characteristics of different pore structures of the soil, and then revealed the effects of pore structure on the removal of heavy metals. The results showed that the soil pore structure of the freeze-thaw washing treatment (FT) became more porous and complex, which increased the soil imaged porosity (TIP), pore number (TNP), porosity of macropores and irregular pores, permeability, and heavy metal removal rate. Macroporosity, fractal dimension, and TNP were the main factors contributing to the increase in TIP between treatments. The porous structure resulted in larger effective pore diameters, which contain a greater number of branching pathways and pore networks, allowing the chemical washing solutions to fully contact the soil, increasing the roughness of the soil particle surface, mitigating the risk of soil compaction, and decreasing the contamination of heavy metals. The results of this study contribute to provide new insights into the management of heavy metal pollution in agricultural soils.