The estimation problem of structured clutter covariance matrix (CCM) in space-time adaptive processing (STAP) for airborne radar systems is studied in this letter. By employing the prior knowledge and the persymmetric covariance structure, a new estimation algorithm is proposed based on the whitening ability of the covariance matrix. The proposed algorithm is robust to prior knowledge of different accuracy, and can whiten the observed interference data to obtain the optimal solution. In addition, the extended factored approach (EFA) is used in the optimization for dimensionality reduction, which reduces the computational burden. Simulation results show that the proposed algorithm can effectively improve STAP performance even under the condition of some errors in prior knowledge.