In existing identification methods for on-orbit spacecraft, such as eigensystem realization algorithm (ERA) and subspace method identification (SMI), singular value decomposition (SVD) is used frequently to estimate the modal parameters. However, these identification methods are often used to process the linear time-invariant system, and there is a lower computation efficiency using the SVD when the system order of spacecraft is high. In this study, to improve the computational efficiency in identifying time-varying modal parameters of large spacecraft, a faster recursive algorithm called fast approximated power iteration (FAPI) is employed. This approach avoids the SVD and can be provided as an alternative spacecraft identification method, and the latest modal parameters obtained can be applied for updating the controller parameters timely (e.g. the self-adaptive control problem). In numerical simulations, two large flexible spacecraft models, the Engineering Test Satellite-VIII (ETS-VIII) and Soil Moisture Active/Passive (SMAP) satellite, are established. The identification results show that this recursive algorithm can obtain the time-varying modal parameters, and the computation time is reduced significantly.