Internal profile nondestructive measurement of MEMS microstructures based on semiconductor materials is urgently demanded with the dramatic development of MEMS industry. A new attempt was made to extend the interferometric method and the thickness-profile measurement theory of transparent thin film layers from the visible light region (400–800 nm) to near-infrared light region (900–1700 nm). The measurement system based on Linnik interferometer using a near-infrared halogen light source with 1127 nm center wavelength was established for internal profile measurement. The measurement method for internal profile of GaAs microstructures was realized. From a comparison of reflection interferometry and transmission interferometry, it can be concluded that the latter measurement results were consistent with those of the former and internal profile was determined within an error range of 8%.