Time-varying parameter identification is essential for structural health monitoring and performance evaluation. In this paper, a combined method based on the variational mode decomposition and generalized Morse wavelet is proposed to identify the structural time-varying parameters. Based on the sparse property of structural response signals in wavelet domain, a fast iterative shrinkage-thresholding algorithm is adopted to reduce the noise. Then the de-noised signal is decomposed into multi- modes by the variational mode decomposition, and the generalized Morse wavelet is performed to identify the instantaneous frequency. To validate the proposed method, a numerical example including different frequency variations is studied. Experimental validations of a moving vehicle across a bridge and a time-varying cable system considering two patterns of cable tension variations in the laboratory are carried out to investigate the capability of the proposed approach. It is confirmed that the proposed approach can effectively perform the signal decomposition, while identifying the instantaneous frequencies of the time-varying systems accurately.