The Schwarzschild microscope is suitable for sample navigation in secondary ion mass spectrometry (SIMS) because of its advantages of a simple structure, large working distance, and good coordination with the ion extraction system. The high numerical aperture (NA) of the microscope significantly reduces diffraction effects, but the resulting high-order geometric aberrations seriously affect the imaging quality. In this paper, a novel design method of the Schwarzschild microscope with a high NA (0.47) was proposed. The aberration distributions and compensation methods were investigated through tolerance analysis. The results showed that the tilt and decenter tolerances become the dominant factors limiting the spatial resolution, which could only be improved by ensuring the alignment accuracy of mirrors. Finally, the spatial resolution of the microscope in the home-built SIMS reached 2.19 µm.