This study conducted in-situ vibration tests on the beam bodies of two types of bridges, namely, cable stayed bridge and box girder viaduct, to collect the in-situ vibration signals, which are analyzed by using the Hilbert-Huang Transform method. The nonlinear and non-stationary signals can be processed to purify and extract the real vibration signals needed through the intermittency criterion. The orthogonal index correlation check increases the accuracy of the empirical mode signal decomposition results. Moreover, the damage locations in the bridge beam body structure system could be decided in an effective and fast manner preliminarily through the time, speed and distance transformation in the Hilbert spectrum diagram. Finally, the beam body damage locations are confirmed in an accurate and stable manner in cooperation with the on-site inspection and verification so that the management authorities can quickly determine the bridge conditions.