Iterative learning control (ILC) is an important method for networked control systems and it uses the control information several times before to form the current control input signal [1]. Nowadays, ILC has developed maturely, but its output signal may cannot track the desired trajectory accurately because of the channel noise of wireless transmission. In this paper, we introduce the Adaptive Fourier Decomposition (AFD) algorithm to eliminate the channel noise superimposed on the output signal in the wireless transmission process [2]. So an ILC method for discrete linear system with wireless transmission based on AFD in frequency domain is proposed. The simulation results show that the AFD algorithm is able to achieve signal denoising well in the case of small decomposition threshold compared with Fourier decomposition, and then the goal that the output signal of ILC system can track the desired signal accurately will be achieved.