Cracking behaviors and its influence on the hydraulic properties are of paramount importance in reservoir engineering and geotechnical engineering, and rare studies focus on the failure process of geomaterials and its effect on the transport properties with fractural microstructures. Therefore, a double threshold segmentation algorithm is proposed to obtain the crack-pore-grain microstructures in this paper, and the cracking behaviors and evolution process of cracks are studied based on these microstructures. In addition, a single-phase flow is simulated to evaluate the effect of fractures on the transport properties in fractural microstructures. This approach is helpful to understand the failure mechanism and the influence of fractures on the transport properties of geomaterials at microscale, which provides an excellent tool to study the fractural and hydraulic properties.