The cracks caused by drying and shrinkage in farmland affected the soil hydraulic and physical structure characteristics and provided preferential channels for the transport of irrigation water or pollutants. In order to reveal the evolution characteristics of crack morphology and shrinkage of matrix in farmland and predict the crack porosity, experiments were carried out in a greenhouse. Digital image processing and morphological algorithm were used to analyze the geometric characteristics of cracks during the dry-wet cycle.Non-invasive local shrinkage analysis method was used to quantify the shrinkage characteristics of matrix domain. According to the transformation mechanism of soil pores from matrix domain to subsidence domain and crack domain during dewetting process, a prediction model of soil crack porosity was proposed, which included two submodels: VG-PENG model and Logistic function of shrinkage geometric factor. Based on the measured crack porosity experiment, the universal applicability of the model was verified for the crack porosity of soil samples of different thicknesses. From the perspective of soil physics, the evolution process of crack porosity with respect to water content was effectively predicted. The results showed that layer thickness had significant influence on crack morphology during soil cracking. With the increase of soil layer thickness, the width of large cracks on the surface of the reconstituted soil was increased, the possibility of secondary cracking was decreased, and the density of cracks was decreased, and the process of soil shrinkage and cracking was slowed down. In the process of drying and shrinking, the soil showed the phenomenon of agglomeration to block core. The minimum value deformation near the core in the shrinkage block area tended to be 0, and the edge wall area of cracks showed a concentrated deformation area, and the shrinkage was increased with the increase of soil layer thickness. The vertical uniformity of drying rate and drying degree also changed with soil layer thickness. Thicker soils usually had wider cracks in the soil surface and larger clumps of soil formed by cracking. In the cracking process, the shrinkage anisotropy showed vertical subsidence in the first stage, vertical subsidence in the middle stage with slight horizontal shrinkage, and horizontal cracking in the late stage. Considering the anisotropy of soil shrinkage, the prediction model of crack porosity proposed made up for the shortcoming that the previous crack models did not consider the shrinkage anisotropy, and the model had good effect and was generally applicable in different soil thicknesses (R2>0.91). The study quantified the development characteristics of crack and matrix at soil samples of different thicknesses, which provided the parameter basis for the construction of crack flow model and the hydraulic characteristics of soil matrix, and contributed to the formulation of expanded soil remediation and water management schemes.