Using aggregate generation and packing algorithm technique coupled with finite element method, a part of reconstructed asphalt pavement structure with five layers and containing a bottom-up crack was simulated. For more realistic modeling and more accurate analyzing the cracking behavior of pavement, a region surrounding the initial crack (and bottom-up crack) region and its neighborhood was modeled as a heterogeneous two-phase (aggregate/mastic) mixture. The results of numerical analyses showed that a significant difference exists between the crack tip fracture parameters (i.e., KI, KII, Keff, T-stress, and Biaxiality ratio) of the homogenous and heterogeneous models. The heterogeneous simulation (in this case study) leads to approximately 70% reduction in the effective stress intensity factor. Furthermore, it was shown that the fracture trajectory of a simulative reflective cracking (SRC) test conducted on a real bilayer asphalt beam sample can be predicted well by modeling the beam layers as a heterogeneous two-phase mixture.