This paper introduces a new method for reconstructing virtual two-dimensional (2-D) microstructure of hot mix asphalt (HMA). Based on the method, the gradation of coarse aggregates and the film thickness of the asphalt binder can be defined by the user. The HMA microstructure then serves as the input to the computational fluid dynamic (CFD) software (ANSYS-FLUENT) to investigate the water flow pattern through it. It is found that the realistic flow fields can be simulated in the 2-D micro-structure and the flow patterns in some typical air void structures can be identified. These flow patterns can be used to explain the mechanism that could result in moisture damage in HMA pavement. The one-dimensional numerical permeability values are also derived from the flow fields of the 2-D HMA microstructure and compared with the measured values obtained by the Karol-Warner permeameter. Because the interconnected air voids channels in actual HMA samples cannot be fully represented in a 2-D model, some poor agreements need to be improved.