A numerical simulation study on the rainfall infiltration characteristics of unsaturated fractured soil was performed based on COMSOL Multiphysics software. By discretizing the fracture and the matrix into finite elements, a discrete fracture-porous medium model was established to fully simulate the fracture flow, matrix flow and fracture–matrix flow exchange in the soil. The upper boundary of the fractured soil was simulated by using the concept of “air element”. This method can describe not only the phenomenon of preferential infiltration for rainwater along the fractures at the beginning of rainfall, but also the phenomenon of rainwater flowing away along the surface when the rainfall is greater than the infiltration of the fractured soil. By simulating the low-permeability fractured soil at a depth of 2 m below the ground surface, the influences of the geometric characteristics of the fracture, the hydraulic properties of the matrix, the previous moisture condition and the rainfall intensity on the rainfall infiltration process of the unsaturated fractured soil were investigated. The results show two main seepage processes in the unsaturated fractured soil: firstly, water flows preferentially along the fracture; secondly, water is continuously imbibed into the matrix from the fracture, and the matrix imbibition inhibits the development of preferential flow in the fracture. Compared with the geometric characteristics of the fracture, the hydraulic properties of the matrix have a greater influence on the seepage flow in the unsaturated fractured soil. Increasing the saturated permeability coefficient of the matrix may change the seepage flow dominated by the fracture flow into that dominated by the matrix flow. The unsaturated properties of the matrix as well as the initial water content of the fractured soil change the soil moisture storage capacity, thereby accelerating or delaying the time for rainwater to infiltrate into a certain depth. The rainfall intensity has an influence on both the infiltration rate and infiltration amount in the soil. When it exceeds the infiltration capacity of the fractured soil, the excess rainwater flows away along the surface, and the infiltration rate across the section tends to stabilize with time.