In this paper, the consensus problem of multi-agent systems with two-layer network topology under intermittent communication mechanism is studied. Firstly, a consensus control protocol based on intermittent communication mechanism is proposed. By modeling the network structure and establishing the error system model, the consensus problem is equivalent to the asymptotic stability problem of linear time-delay systems. Secondly, by using Lyapunov-Krasovskii functional analysis method, the sufficient conditions for multi-agent networks to reach consensus under intermittent communication mechanism are derived, and the conclusions are given in the form of a set of LMIs. Finally, a simulation example is given to verify the effectiveness of the proposed method.