The invention discloses a structured light illumination microscopic measurement method for multi-layer micro-nano structure detection. According to the method, a digital micromirror array (DMD) is adopted to generate a coded light field, and the coded light field is projected onto the surface of an object to be measured; a CCD is adopted to collect the reflected light intensity information of eachlayer structure; a phase shift algorithm and a two-dimensional Fourier transform algorithm are combined so as to perform analysis to obtain the modulation degree distribution of an acquired image; apiezoelectric ceramic (PZT) is adopted to vertically scan the object to be measured, so that modulation degree curves corresponding to each pixel point are obtained; and the peak values of the modulation degree curves are extracted, so that the shape detection of the multilayer micro-nano structure can be realized. With the method adopted, the influence of noises on the extraction of the peak values can be suppressed effectively, and the shape information of the object to be measured can be retained. The method has the advantages of simple measurement system, wide measurement range and small interference between the signals of a plurality of layers of structures.