Compared with traditional hot mix asphalt (HMA), wax based warm mix asphalt (WWMA) can be mixed with the aggregate at a lower temperature and achieve the desired compaction. However, the adhesion performance of WWMA on aggregate is uncertain. To evaluate the adhesion performance of asphalt and aggregate, researchers used contact angle test, pull-off test, and ultrasonic washing experiments. However, these tests cannot adequately explain the microscopic mechanism of the interface between asphalt and aggregate. Molecular dynamics (MD) can better explain the adhesion mechanism of asphalt aggregates because they can be simulated at the molecular scale. So, the purpose of this research is to use the MD method to study the adhesion performance between WWMA and aggregate. Two aggregate oxides (CaCO3 and SiO2) models, the matrix asphalt model and WWMA models, were built in Materials Studio (MS) software. The adhesion work of asphalt and aggregate oxides was calculated. With the increase of wax modifier content, the adhesion work of asphalt and aggregate oxides (CaCO3 and SiO2) first increases and then decreases. When the wax modifier is increased to 3 wt%, the adhesion works of the WWMA-SiO2 and WWMA-CaCO3 increase by 31.2% and 14.0%, compared with that of matrix asphalt. In this study, the accuracy of the MD calculation result was verified by the pull-off experiments and the contact angle experiments. WWMA was prepared by a high-shear mixer emulsifier. In the pull-off experiments and the contact angle experiments, the tensile strength and the adhesion work between the aggregate and the asphalt containing 3% wax modifier reaches peak values. These values are 140.7% and 124.9%, compared with those between the aggregate and the matrix asphalt. In addition, the results of the pull-off experiments and the contact angle experiments are in good agreement with that of the MD simulation. Finally, Fourier transform infrared spectroscopy (FTIR) shows that the carbonyl content of WWMA is greater than that of matrix asphalt. It explains well that the wax modifier promotes the adhesion between asphalt and aggregate. This paper provides an important theoretical basis to understand the adhesion performance of WWMA and aggregate.