Disclosed herein is a method for non-destructive hybrid acousto-optic and scanning electron microscopy-based metrology. The method includes: (i) obtaining acousto-optic and scanning electron microscopy measurement data of an inspected structure on a sample; (ii) processing the measurement data to extract values of key measurement parameters corresponding to the acousto-optic measurement data and the scanning electron microscopy measurement data, respectively; and (iii) obtaining estimated values of one or more structural parameters of the inspected structure by inputting the extracted values into an algorithm, which is configured to jointly process the extracted values to output estimated values of the one or more structural parameters.