The development of precision manufacturing has put forward a higher requirement for the 3D topographical measurement of complex microstructures. It is a little difficult for the existing non-contract measurement method to measure a slope surface with a big gradient although it has a high vertical solution. In recent years, the focus variation measurement method based on ultrashort depth-of-field imaging performs well in the measurement of tilted surface and can be used to truly realize the 3D surface measurement of a microscopic complex structure. Firstly, the principle of microscopic 3D measurement based on focus variation is summarized. Then, the latest theoretical and technological research progress on this method is addressed. Finally, the challenge and future development trend of microscopic 3D measurement based on focus variation are discussed and prospected.