Traditional polymer modifiers and asphalt are often blended by physical melt blending. In the process of use, problems such as segregation, poor compatibility and storage stability are prone to occur. Polyurethane prepolymer is rich in characteristic functional isocyanate groups, has strong group chemical activity, and can form three-dimensional cross-linked interpenetrating network structure with asphalt, which has significant advantages in the preparation of high-performance modified asphalt. In this paper, the polyurethane prepolymer modified asphalt was systematically reviewed. Firstly, a concise summary was provided on the synthesis principle of polyurethane prepolymers. Subsequently, a detailed description was given on the preparation process of its modified asphalt and performance in both modified asphalt and asphalt mixtures. Finally, an in-depth analysis was carried out to uncover the micro-mechanism of its modified asphalt, thereby revealing its macro-micro characteristics. Additionally, the advantages and existing problems of polyurethane prepolymer modified asphalt were summarized, and future research directions and trends in the field of its modified asphalt were identified, with the goal of enhancing its application level in engineering practice.