As is well known, complex networks in reality are usually interconnected. To describe the interconnected networks, multiplex networks were presented recently. In this brief, an aperiodically intermittent pinning control scheme is put forward to realize cluster exponential synchronization in a two-layer (leader-follower) network with multi-links and time-varying delays. Based on the principle of intermittent control and Lasalle invariant principle, some criteria for cluster synchronization are deduced by theoretical analysis. Numerical simulations are provided to verify the effectiveness of the proposed scheme. In comparison with the previous methods, our model better describes the real-world networks and our control effectively reduces the control cost.