This paper is concerned with distributed consensus control of unknown multiagent systems. As the system’s dynamics is unknown, an adaptive Fourier decomposition (AFD) based iterative learning control (ILC) dynamics adaptive matching method in frequency domain is put forward to deal with it. First, large amounts of input and output measurement data are used to estimate the frequency domain characteristics of the system by Takenaka-Malmquist functions. Second, convert the traditional time domain ILC to the frequency domain to establish a matching relationship with the estimated frequency domain features. Then, an adaptive iterative learning rate is constructed to achieve the optimal convergence at each sampling point. The feasibility of the proposed algorithm is guaranteed by the convergence of AFD in Hardy space $H^{2}(\mathbb {D})$ under the maximum selection principle. Compared with the reinforcement learning data-driven control scheme, the method proposed in this paper has obvious advantages in the control accuracy and convergence efficiency. In addition, this paper takes two kinds of denoising algorithms based on unwinding AFD to deal with the multi-agent systems with channel noise. Finally, the feasibility and effectiveness of the developed method are verified by a series of simulations.