In this paper, on-orbit modal identification of membrane antenna spacecraft is investigated. Based on the modal identification results, dynamic model of the spacecraft is updated, and a vibration controller is designed. First of all, the rigid-flexible coupling dynamic model of the membrane antenna spacecraft is established by using Lagrange equation. Then, the covariance driven stochastic subspace identification (SSI-COV) method, which only relies on output measurements of the system under ambient excitation, is adopted to identify the modal parameters. By using the modal identification results, the model updating is performed based on sensitivity analysis, and vibration controller is designed to suppress the vibration caused by attitude maneuver based on the component synthesis vibration suppression (CSVS) method. Simulation results show that the SSI-COV method can identify the modal parameters of the membrane antenna spacecraft effectively, the updated dynamic model produces obvious improvements over the original model, and the vibration suppression effect of the CSVS controller is improved significantly after model updating.