In order to study the compatibility between the rubber powder and the asphalt in the rubber powder modified asphalt, the four component representative molecular model of asphalt and the representative molecular model of rubber were constructed by Materials Studio. The asphalt molecular group was constructed based on the four component analysis experiment. The solubility parameters and molecular potential energy at different temperatures were obtained by molecular dynamics calculation of the asphalt molecular group model and rubber representative molecular model at different temperatures. The results show that the solubility parameters of asphalt system decreases with the increase of the temperature; the differences of solubility parameter between the asphalt group molecular and the rubber representative molecular—styrene butadiene rubber(SBR) are on the minimum, but the potential energy between the asphalt group molecular and the rubber molecule reaches the maximum, indicating that the asphalt and the rubber powder achieves the best phase state at 160℃, therefore rubber powder modified asphalt achieves the best compatibility and stability.