Micro/nano structures with multilayer features have been widely applied in the fields of display, semiconductor, MEMS. The existing methods based on phase analysis of interferogram including white-light interferometry and spectral interferometry utilize the phase information of interferogram formed by multilayer reflected light and reference light to achieve multilayer three-dimensional reconstruction. However, when the number of dielectric layers is large, the interference signals of adjacent dielectric layers will interfere each other, which seriously affect the measurement accuracy. Also, there are various limitations in the measurement of complex structures with large steps and high curvatures. The measurement method based on the modulation evaluation of structured light is a unique way in the field of complex micro-nano structure measurement due to its non-contact, high precision, high adaptability. The principle of structured light to synchronously realize the three-dimensional reconstruction of multi-layer structure is applied in this paper. By imaging different dielectric layers, the modulation degree distribution of different layer structures is analyzed, and finally the multi-layer structure and its thickness distribution are synchronously measured in three dimensions.