Abstract: Optical window of remote sensing system has thermal exchange with ambient environment and it causes non-uniformity thermal distribution, including system average temperature shift as well as circumferential, radial and axial temperature differences, which degrade the image quality. A new method was presented to analyze this effect on the optical system wavefront error by building segments made up of complex pupils. Each segment can be effectively analyzed because of only the radial temperature being processed by non-sequential ray trace. Then all the separate impacts of the segments were calculated on the entire optical window. An example of the optical window is given, and the result shows that the method is feasible, the optical system quality is reduced by this effect and its MTF can not be completely compensated by focus shift.