Disclosed are a thin flat plate structure resonance modal analysis system and a using method thereof. The system comprises a first beam splitter prism, a first space light filter, a second space light filter, a second beam splitter prism, an optical signal camera, a PC (personal computer) and a frequency-tunable sine wave generator, the first beam splitter prism is positioned on a laser outlet side of a laser light source, the first space light filter is positioned on one side of an object beam of the first beam splitter prism, the second space light filter is positioned on one side of a reference beam of the first beam splitter prism, a detected flat plate for receiving light is arranged on a light emergent side of the first space light filter, a reference plane for receiving light is arranged on a light emergent side of the second space light filter, an image acquisition card which is used for receiving images acquired by the camera is embedded in the PC, and an output end of the frequency-tunable sine wave generator is connected to a shock excitation source for performing shock excitation for the detected flat plate. The system can precisely detect micrometer resonance deformation. Coordinate values of the most severely deforming position of the thin flat plate and the deformation maximum value can be solved one by one by a later-stage image processing method.