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The increase of the time-step size significantly deteriorates the property of the coefficient matrix generated from the Crank-Nicolson finite-difference time-domain method. As a result, the convergence of classical iterative methods, such as generalized minimal residual method (GMRES) would be substantially slowed down. The main purpose of this article is to show that the two-step preconditioner can greatly accelerate the convergence of the iterative method, such as GMRES. Numerical simulations show that this two-step preconditioned GMRES iterative method has a faster convergence speed than those methods when the preconditioner is used alone.