In order to describe the crack development of epoxy asphalt concrete (EAC) from the three-dimensional (3D) scale perspective, a 3D virtual specimen of EAC with the heterogeneous (coarse aggregates, asphalt mastic and air voids) and multilayer (aggregate gradation) morphological features was first reconstructed by using the Fish language provided in the discrete element software PFC3D. Secondly, the corresponding micromechanical models describing the interaction of micro-scale components of the virtual specimen were assigned. Finally, a single-edge notched beam virtual three-point bending test was implemented by using the discrete element method (DEM). The progressive development of microcrack trajectories was tracked and visualized, and the simulation results were compared with the surface crack development of specimens captured in a digital camera method. The results have indicated that the macro fracture responses of virtual test show generally good agreement with the experiment results, and the virtual test presents better stability than the laboratory test. Additionally, the three-dimensional DEM developed is capable of simulating the initiation and propagation of cracks during the bending fracture of EAC, thus improving the two-dimensional (2D) method. Furthermore, it has been found that the method based on the DEM program, which is used to illustrate the development of 3D cracks, can be used as a supplemental tool to investigate the fracture behavior of EAC.