Top-down cracking (TDC) has been well recognized as a major distress for the heavy duty asphalt pavements yet the mechanism is still not fully understood. Studies indicated the non-uniform tire-pavement contact stress might play a significant role in the initiation of TDC, and thermal stress due to temperature gradient might contribute to the initiation and development of TDC. For this concern, a sophisticated three-dimensional (3-D) viscoelastic finite element model was developed to study cracking performance of heavy duty flexible pavements under combined 3-D tire-pavement contact stress and thermal stress induced by temperature gradient. It was found the stress distribution in asphalt concrete (AC) layer is continuously changing as the pavement is loaded due to rheological behavior of AC. Significant maximum principal tensile stresses are presented at the edge of tire at AC surface, which may result in an accumulation of dissipated creep strain energy (DCSE) over time (or with number of loads) and may eventually lead to the initiation of a crack. And pavement near-surface responses associated with top-down cracking under 3-D tire-pavement contact pressure is more severe as compared to uniform contact pressure. Comparing with pavements without thermal effect, the negative temperature gradient increases the potential for top-down cracking while the positive temperature gradient increases the potential for bottom-up cracking. The study may provide some meaningful insight into crack mechanisms and help improve current heavy duty asphalt pavement design procedures for cracks.