Earthen sites are easily eroded by the natural environment, resulting in a large number of micro cracks on the surface. In order to explore the internal relationship between environmental factors and the cracking law of soil sites, this paper carries out dry shrinkage tests of different soil layers at the Zhouqiao site, reconstructs the study on cracking law of earthen soil under dry shrinkage-conditioned microstructure of site soil at different depths based on electron microscope pictures and finite element method, and explores the influence of different moisture content on the cracking of soil samples at the site. The results show that under conditions of dry shrinkage, the thickness of the soil layer has the greatest influence on the cracking of site soil samples. Due to the internal water loss and shrinkage of the soil sample, the thinner the soil layer, the more often the soil layer cracks first. The crack rate of the soil sample with a thickness of 1 cm is nearly three times higher than that of the soil sample with a thickness of 5 cm. Through numerical simulation analysis, it is found that the evolution process of soil fractures at the Zhouqiao site is mainly divided into the formation stages of initial stress field, single main fracture, secondary fracture and fracture network. The formation time of the secondary fracture is longer than that of the initial stress field and single main fracture, and the cracking of the upper soil sample is more serious than that of the lower soil sample. Under conditions of dry shrinkage, the particle arrangement of the soil sample is relatively loose, and there are many cracks inside, which provides evaporation and infiltration channels for water, forming unrecoverable weak pores, and finally, the cracks start to sprout at the weak points. The research results provide some reference for the disease mechanism and safety analysis of earthen sites.