Aerodynamic noise contributes dominantly to automotive interior and exterior noise, especially when driven at high speed. Transmitted through side window, it causes great influence on comfortability and NVH (Noise-Vibration-Harshness) performance. However, the complicated external turbulent air flow, as well as the internal metal-rubber nonlinear sealing constraint, makes the mechanism of aerodynamic noise generation and transmission very difficult. An efficient two-step methodology has been proposed regarding the complex load situation and boundary condition during numerical prediction. The first step involves the model-based CFD (Computational Fluid Dynamics) analysis and Lighthill’s noise source theory. External turbulent flow field of full-scale automotive is established by solving three-dimensional, steady and uncompressible Navier-Stokes equation. Transferring spatial flow velocity gradient by aeroacoustics analogy equation, side window near-field sound pressure distribution has been obtained to investigate the noise generation mechanism. The second step consists in the numerical prediction of noise transmission. New nonlinear spring-based surrogate model for seal constraints is proposed by functional equivalence. Modal experiment was conducted to verify the effectiveness of sealing surrogate strategy. Using vibro-acoustic solver Actran, FEM (Finite Element Model) for aerodynamic noise transmission integrating nonlinear sealing system has been established. Based on the sound-proof mass law, new side window structural design by non-uniform density distribution is proposed to optimize the STL (Sound Transmission Loss) property.