High aspect ratio (HAR) microstructures are widely used in fields of microelectromechanical systems (MEMS) and three-dimensional integrated circuits (3D-IC). Depth of HAR structures, as one of the key functional features, largely determines both the performance of micro and nanostructured sensors and the process difficulty. In particular, the process trend of HAR exacerbates the scale effect and triggers defects such as filled voids and defects, resulting in poor depth uniformity, which greatly affects the actual performance of the device. Therefore, it is essential to develop a reliable method for accurately inspecting the depth of HAR microstructure, especially in-line inspection. However, traditional reflection spectroscopy measurements face a significant challenge due to the sharp attenuation of the optical signal returned from the bottom of the structures. In this study, we propose an optical measurement method that utilizes reflection spectroscopy to easily measure the depth of very deep HAR trenches. The system comprises flexible fiber optic rays, which effectively achieve a ultra-low numerical aperture (NA) during the measurement. This improvement enhances the interference contrast of the reflection spectra. Additionally, a telecentric lens with a camera is used to image the microregion and locate the measurement position. For demonstration, we measured a single trench using the homemade system, and successfully verified that the system can measure structures with a measurable high aspect ratio up to 50:1 and a measurable depth of over 400 mu m. Overall, our proposed optical measurement method offers a reliable solution for inspecting the depth of HAR microstructures, enabling improved device performance and process control.