Automotive window seal has great influence on NVH (Noise-Vibration-Harshness) performance. The aerodynamic effect on ride comfort has attracted increasing research interest recently. A new method for quantifying and transferring aerodynamics-induced load on window seal re-design is proposed. Firstly, by SST (Shear Stress Transport) turbulence model, external turbulent flow field of full scale automotive is established by solving three-dimensional, steady and uncompressible Navier-Stokes equation. With re-exploited mapping algorithm, the aerodynamics pressure on overall auto-body is retrieved and transferred to local glass area to be external loads for seals, thus taking into account the aerodynamics effect of high speed fluid-structure interaction. This method is successfully applied on automotive front window seal design. The re-design header seal decreases the maximum displacements of leeward and windward glass with 9.3% and 34.21%, respectively. The improvement of fitting stability shows the effectiveness this seal re-design considering high-speed fluid-structure interaction.