A methodology for simulating groundwater flow in three-dimensional (3D) stochastic fracture rocks based on a commonly used finite-difference method is presented in this paper. Different realizations of fracture networks are generated by the fracture continuum method (FCM), in which appropriate 3D cuboids are used to describe the geometry of fractures. Then, the effects of different parameter distributions on the fracture networks indicated that the length, orientation, and density of fractures all play significant roles in the connectivity of fractures in this methodology. Greater length and density and wider orientation range of fractures lead to greater connectivity. The proper contrast in hydraulic conductivities between the fractures and matrix is found to be approximately 105 due to the contribution of fluid flow in the matrix which can be ignored. It is shown that the fracture density plays a key role in stabilizing the equivalent hydraulic conductivity (Ke) of the fracture networks. Furthermore, the greater length and closer orientation of fractures to the general flow direction, the larger Ke of the generated fracture networks possess. The findings of this study can help for a better understanding of the mechanism of FCM and the influence of geometry characteristics on the hydraulic conductivity of FCM models.