Aiming at the requirements of high resolution and high imaging quality of the microscope system, the general number of pieces of the system is difficult to adjust, so that the system is difficult to match the actual adjustment result and the design result. Therefore, the lower aberration compensation design method was proposed to design the system. At the same time, the sensitivity of each optical component in a system could be reduced. First, a mathematical model of the lower aberration compensation design method was established, and then it was written into ZEMAX programming language (ZPL) macro that could be used to control ZEMAX to optimize the optical system. Finally, an infrared microscope system was taken as an example. Comparing the optimization results before and after the implementation of the lower aberration compensation design method, it was validated that the proposed method was efficient. It is found that the optical system using the lower aberration compensation design method has an outstanding advantage in image quality comparing with the conventional method. The tolerance sensitivity of each component is significantly reduced, thereby improving the stability of the overall optical system effectively.