A dynamic 3D nano-scale surface profilometer was successfully developed for novel automatic resonant frequency identification using stroboscopic interferometric principle. With rapid increase in the application of micro electromechanical systems (MEMS) to industries, the needs of accurate dynamic characterization have become a major challenge in design and fabrication. In view of such, an interferometric microscopy was developed using LED stroboscopic interferometry to achieve dynamic full-field profilometry and characterization of MEMS with a measurement bandwidth exceeding 1 MHz. Most importantly, a novel detection algorithm was also developed employing interferogram fringe density measure for automatic resonant frequency identification. Natural resonant modes of a series of microstructures can be accurately detected, giving values consistent with theoretical ones. To verify the effectiveness of the developed methodology, an AFM cantilever microbeam and a cross-bridge microbeam were measured to analyze their full-field resonant vibratory shapes. Our experimental results confirmed that the resonant vibration of the tested beams can be fully characterized while achieving an accuracy in vertical measurement of 3–5 nm with a vertical measurement range of tens of micrometers.