Fault zones and fault-related fracture systems control the mechanical behaviors and fluid-flow properties of the Earth’s crust. Furthermore, nowadays, modeling is being increasingly used in order to understand the behavior of rock masses, and to determine their characteristics. In this work, fault zones and fracture patterns are reviewed, and also comprehensive studies are carried out on the fracture geometry and density variations. A model to describe damage zones around the strike-slip faults is developed, in which the range of damage zone styles commonly found around strike-slip fault zones are shown. A computer code, named DFN-FRAC3D, is developed for the two- and three-dimensional stochastic modeling of rock fracture systems in fault zones. In this code, the pre-existing and fault-related fractures are modeled by their respective probability distributions, and the joint density may be varied by the distance from the fault core. This work describes the theoretical basis and the implementation of the code, and provides a case study in the rock fracture modeling to demonstrate the application of the prepared code.