Soil pollution may cause great harm to human health and ecological environment. Improvement of simulation accuracy for contaminant transport in soil, is an important precondition of pollution control and remediation. Previous studies have shown that soil structure and scale difference have significant influences on contaminant transport. In order to quantitatively analyze the influence of the above differences on the prediction results, four spliced Sierpinski fractal carpet model was constructed to simulate the soil structure based on the establishment of a single Sierpinski fractal carpet model, to investigate the influences of fractal structure and spatial scale on the diffusion behavior, and the boundary effect of fractal structure was discussed emphatically. By analyzing the particle random walk in two kinds of fractal structures, the spatial displacement, density distribution and mean square displacement in different fractal structures are obtained. The results of numerical simulation show that the diffusion behavior is sub-diffusion in the single fractal structure with small scale when the diffusion process is not affected by boundary restrictions. When the diffusion process of particles is affected by the boundary effect, the diffusion behavior changes from sub-diffusion to normal diffusion in a short time period. However, the boundary has little influence on the diffusion process in the spliced fractal structure with large scale. In addition, the diffusion behavior is sub-diffusion and keeps stable for a long time period.