When a hypersonic seeker flies at high speed within the atmosphere, intense interaction with the incoming flow gradually develops into a complex turbulent flow field. This interaction results in complex thermal responses at the seeker window, causing aerodynamic optical effects such as image shift, jitter, and blur of the target image, thereby restricting the seeker's detection capability and accuracy. This paper uses a numerical simulation model for the guidance performance of a hypersonic seeker under aerodynamic optical transmission effects. The study focuses on an ellipsoidal seeker, with its supersonic flight simulation on the basis of the Reynolds-Averaged Navier-Stokes (RANS) equations to get a non-uniform gradient flow field. The correctness of the flow filed results can be verified by wind tunnel experiments. The transient temperature field of the seeker is solved using an unsteady thermal conduction-radiation coupled fluid-solid heat transfer method. Finally, the guidance performance of the hypersonic seeker under aerodynamic optical effects is predicted using the ray tracing method, which employs wavefront aberration, point spread function, degraded images, and image shift.