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In this research, a sub-array preconditioner is applied to improve the convergence of conjugate gradient (CG) iterative solver in the fast multipole method and fast Fourier transform (FMM-FFT) implementation on a large-scale finite periodic array antenna with arbitrary geometry elements. The performance of the sub-array preconditioner is compared with the near-group preconditioner in the array antenna analysis. It is found that the near-group preconditioner achieves a little better convergence, while the sub-array preconditioner can be easily constructed and programmed with less CPU-time. The efficiency of the CG-FMM-FFT with high efficient preconditioner has been demonstrated in numerical analysis of a finite periodic array antenna.