High-power ultrasound significantly enhances the dispersion of high-viscosity liquids and concentrated suspensions. When applied to modified asphalt, it promotes polymer particle refinement and improves phase compatibility. In this study, crumb rubber modified asphalt was fabricated using an ultrasonic synergistic high-speed shearing technique. The influence of this combined process on the asphalt’s properties was systematically evaluated through a series of tests, including penetration, softening point, ductility, viscosity, self-healing capability, contact angle measurements, and micro morphological analysis. Molecular dynamics simulations were conducted to analyze the relative concentration distribution of water and asphalt, debonding work, energy ratios, and hydrogen bond variations within the asphalt–water–aggregate interface model. The results indicate that ultrasonic-synergistic shearing technology effectively suppresses agglomeration in rubber-modified asphalt, significantly improves two-phase compatibility, reduces penetration, and enhances self-healing ability and high-temperature resistance. Moreover, it improves the stability and water damage resistance of the asphalt mixture.