Automotive window seals insulate noise and water leakage, allowing door glass to move smoothly and steadily. Being used repeatedly, it is associated with human sensibility and greatly influences NVH performance. Under high speed driving condition, external aerodynamics leads to additional unsteady load. Its effect on ride comfort attracts increasing interest, which was ignored in previous window seal design. A new method for quantifying and transferring the aerodynamics-induced load on window seal 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 was successfully applied on automotive front window seal design. After obtaining external aerodynamics load, the non-uniform pressure distribution on local leeward and windward glass is obtained. It was transferred to be new additional load for seal cross-section design. The optimal header seal decreases the maximum displacements of leeward and windward glass 9.3% and 34.21%, respectively. The fitting stability improvement shows the effectiveness of new seal design considering high-speed fluid-structure interaction.