Abstract: Infrared windows are dramatically influenced by the separation of interceptor missile shroud cover. Simulations on the interceptor missile shroud covers separation are based on compressible Reynolds Averaged Navier-Stokes (RANS) equations, moving multi-block chimera structure grid technique and finite volume method. The Roe’s Flux Difference Splitting (FDS-ROE) method and a second-order implicit dual-time scheme reconstructed by Lower-Upper Symmetric Gauss-Siedel ( LU-SGS) scheme are involved in solving Navier-Stokes equations. Consequently, the disturbed flow field near the infrared window due to the shock wave interaction during the separation is presented. And the pressure oscillations at different positions on the infrared window are compared. The influence of the flow field on the infrared windows at every time step is captured. Besides, the trajectory of the shroud covers is predicted and the pressure contours during the separation are described.