Recycled glass fibers from wind turbine blades have significant potential for enhancing the performance of asphalt mixtures. However, the impact of residual polyurethane (PU) components on asphalt performance remains uncertain, presenting a challenge to the high-value utilization of wind turbine blades in pavement engineering. This study investigates the effects of waste polyurethane (WPU) on the rheological properties and compatibility of SBS modified asphalt, widely used in pavement engineering under various temperature conditions. Molecular dynamics (MD) simulations were employed to analyze the underlying mechanisms. The results reveal that incorporating WPU improves the rutting factor and creep recovery rate of SBS modified asphalt, demonstrating superior high-temperature performance compared to SBS modified asphalt alone. The synergistic effect of WPU and SBS significantly enhances low-temperature crack resistance and overall asphalt compatibility. Additionally, the interaction between SBS and the four components of asphalt is strengthened, and diffusion mobility is reduced due to WPU incorporation. This indicates that WPU promotes a more compact structure and a higher relative concentration of SBS and the four components within the spatial system, thereby enhancing the stability of the WPU/SBS modified asphalt system. Furthermore, using WPU in asphalt mixtures not only avoids environmental pollution compared to traditional disposal methods but also offers considerable long-term economic benefits. Overall, WPU positively impacts the rheological properties and compatibility of SBS-modified asphalt, suggesting that processed wind turbine blades can be a viable solution for enhancing asphalt mixture performance.