Traditional physical parameter identification methods struggle to analysis the modern multi-degree-of-freedom time-varying (TV) structures. Aiming at this problem, an adaptive reconfiguration algorithm based on polynomial chirplet transform (PCT) is proposed. First, the wavelet basis function of PCT is extracted, and its one-level and tow-level derivative basis functions can be obtained through integral operation. Second, the optimized PCT is applied to the acceleration signal, enabling reconstruction of velocity and displacement signals while establishing their conversion rules. Finally, the vibration differential equation is reformulated, allowing parameter identification. Unlike traditional identification methods, PCT can better track the TV parameters due to the introduction of the frequency modulation slope parameter. Numerical simulations on a three-degree-of-freedom TV structure under varying conditions demonstrate the superior identification accuracy of the proposed method.