In order to improve the accuracy of time-frequency analysis of structural vibration response signals and structural instantaneous parameters identification, the generalized S-transform is improved, and a new form of synchroextracting generalized S-transform is proposed by combining with synchroextracting algorithm. In the numerical simulation, the accuracy of the method is verified by the Duffing nonlinear system with single degree of freedom and the two-layer shear frame structure model. The time-varying cable test is designed, the acceleration response signal of the structure under linear and sinusoidal varying tension is collected. Then, the instantaneous frequency identification of the signal is extracted by improved synchroextracting generalized S-transform, which further verified the accuracy of the method. Numerical simulation and experimental verification show that the improved synchroextracting generalized S-transform can effectively identify the instantaneous frequency of non-linear structures and time-varying structures with good stability.