Abstract: The complicated structure can be divided into several almost regular domains using decomposition domain method (DDM). In this paper, finite difference method(FD)is used to discretize the Helmholtz equation applied with five-points difference discretization. On the regular domain, the fast Fourier transform(FFT)is presented to transform the difference equations to a group of trigonal equations. The theory analysis and numerical results show that the computation complex of this algorithm is about O(PlgP).