During long-term service, asphalt pavements undergo environmental stress and ageing, which cause cracking, rutting, and other distresses and raise maintenance costs. Polyurethane (PU) has high mechanical strength, elastic recovery, and ageing resistance due to its unique molecular structure. As an asphalt modifier, PU has been reported to improve high-temperature stability, moisture resistance, and durability. However, PU and asphalt differ greatly in polarity, density, viscosity, and phase structure, and these differences often lead to segregation and phase separation. The prepolymer method can mitigate these compatibility limitations by adjusting molecular weight, terminal-group activity, and soft/hard segment ratio before dispersion, chain extension, crosslinking, and post-curing in asphalt, resulting in better compatibility and more controllable processing. This review discusses PU soft/hard segment structures, asphalt composition, prepolymer synthesis and curing, microstructural evolution, pavement performance, storage stability, and use in other systems to clarify modification mechanisms and potential applications. This critical review aims to clarify material–reaction–process–performance relationships within the prepolymer route, with scope limited to molecular design, preparation mechanisms, performance, storage stability, and representative engineering applications. Future work should consider real service conditions and build multiscale evaluation frameworks that jointly optimise prepolymer design, processing, storage stability, and pavement performance, helping translate laboratory findings into low-carbon, long-life road materials that can be produced at scale.