The existing coaxial focusing techniques such as critical angle method, Foucault knife-edge test, pinhole method, and astigmatism method are susceptible to the intensity fluctuation and have a high requirement for the system alignment. Therefore, we proposed a novel coaxial focusing method based on differential modulation evaluation. In this technique, the imaging space was first coded by a physical grating. After that, the modulation distribution of the coded image after the substrate height modulation was calculated by the Fourier transform algorithm. Furthermore, the accurate measurement of the substrate height can be realized through combining the modulation with a differential detection system. The theoretical and experimental results demonstrate that the focusing accuracy is better than 10 nm after an objective lens with a numerical aperture of 0.9 and a magnification of 100 is applied. In conclusion, the proposed method does not need any complex optical component and features a simple structure and high testing accuracy, thus providing a novel high-precision coaxial focusing approach for emerging lithography techniques.