According to the non-stationary characteristic of rotating machinery vibration signals of a rotor system with a loose pedestal fault, variational mode decomposition was applied in the pedestal looseness fault diagnosis for such a rotor system. Variational mode decomposition is used to decompose the rotor vibration signal into several stable components. This can achieve the separation of the pedestal looseness fault signal from the background signals, and extract the fault characteristic of a vibration signal from a rotor system with pedestal looseness. Experimental data from a rotor system with pedestal looseness were used to verify the proposed method. The results showed that the stable components of the rotor vibration signal obtained by variational mode decomposition have obvious amplitude modulation characteristics. The components which contain fault information were analyzed by envelope demodulation, which can extract the pedestal looseness fault features of a rotor vibration signal. Therefore, the variational mode decomposition method can be effectively applied to the pedestal looseness fault diagnosis of such a rotor system.