Functional microstructure has the function of regulating light field or electronic conduction, and generally contains regular geometric shapes. Based on the ratio of depth to line width, it can be divided into high/low-aspect-ratio microstructures. At present, the detection of the geometric characteristic parameters of the microstructure is mainly conducted by SEM, which belongs to the destructive detection. The production line urgently needs non-destructive testing technology to monitor and improve its manufacturing process. This article systematically summarizes the progress made by the author's research team in the low-coherence microscopic-interference technology for nondestructive testing of three-dimensional (3D) morphology of microstructures in the past ten years. The white light microscopic interferometer is used to detect the 3D topography of ultra-smooth surfaces, steps, micro optical elements, micro mechanical elements and other low aspect ratio microstructures. A near-infrared micro interferometer is used to detect the 3D morphology of silicon based high aspect ratio microstructures. In this paper, the key technologies of the two band microscopic interference system and the tests of typical samples are described. The results show that white light micro interferometer and near-infrared micro interferometer are two kinds of high-precision nondestructive testing instruments. They can detect the 3D morphology of the microstructures with aspect ratio ≤4, and ≥20, respectively. The 3D topography data obtained by the microscopic-interference nondestructive testing technology will effectively promote the optimization of the manufacturing process of the microstructure and the further improvement of the performance of related devices.