Abstract: In order to solve the shipboard radar antenna mutual interference problem, accurate analysis of the electromagnetic compatibility of shipboard antenna is often required. Based on the method of moments （MoM）， this paper introduces the multilevel fast multipole algorithm （MLFMA） technology and constructs a two step preprocessor in the spectrum domain by combining generalized minimum residual （GMRES）method to accelerate matrix-vector multiplication. The software FEKO is also applied to the electromagnetic modeling on a destroyer, where the algorithm of electromagnetic model of radar antenna pattern and the numerical simulation of the coupling between the antenna are implemented. The results show that the presented algorithm has a higher computing speed and accuracy as well as less memory footprint than the original algorithm, which significantly reduces the number of equation iterations and improves the convergence of matrix equations.