The aero-optical effects of an optical seeker with a supersonic jet for hypersonic vehicles in near space were investigated by three suites of cases, in which the altitude, angle of attack, and Mach number were varied in a large range. The direct simulation Monte Carlo based on the Boltzmann equation was used for flow computations and the ray-tracing method was used to simulate beam transmission through the nonuniform flow field over the optical window. Both imaging displacement and phase deviation were proposed as evaluation parameters, and along with Strehl ratio they were used to quantitatively evaluate aero-optical effects. The results show that aero-optical effects are quite weak when the altitude is greater than 30 km, the imaging displacement is related to the incident angle of a beam, and it is minimal when the incident angle is approximately 15°. For reducing the aero-optical effects, the optimal location of an aperture should be in the middle of the optical window.