Abstract To improve the space‐time adaptive processing (STAP) performance of airborne radar in complex environment, a generalised eigenvalue reweighting covariance matrix estimation algorithm called GERCM is proposed here. First, the interference plus noise (IPN) covariance matrix of cell under test (CUT) data is estimated by the selected target‐free training samples around the CUT with the sample covariance matrix method. Then, with the component decompositions of the selected training samples and the assumption of approximately equal subspace, the IPN covariance matrix of CUT data is reformulated by the eigenvector matrix, eigenvalue matrix, and the eigenvalue reweighting vector. Subsequently, based on the modified covariance matching estimation criterion, the eigenvalue reweighting vector is estimated by solving the redesigned convex optimisation problem with the Lagrange dual method. Finally, the STAP weight vector is calculated to process the CUT data. The proposed algorithm can obtain a relatively accurate IPN covariance matrix of CUT data by sufficiently utilising the non‐homogeneous training samples and can effectively protect the moving targets in CUT data, which can be applied to airborne radar with arbitrary array structure and antenna configuration. Simulation results and performance analyses based on the multi‐channel airborne radar measurement data demonstrate the effectiveness of the proposed GERCM algorithm.