<p>Lag consensus refers to a particular wait-and-track collective dynamic in complex networks and intelligent transportation systems, where every follower’s relative state falls behind the leader with one tracking time delay. In this paper, lag consensus is investigated with different tracking time delays for nonlinear multiagent systems on two-layer networks by pinning control schemes. These control schemes could decrease the node complexity for the two-layer dynamical networks, which means that only partial agents are activated in the subnetwork of each layer. Considering the impact of the dynamic environment and parameter uncertainty on the controlled system, the time-varying tracking time delay is more realistic; thus, a feedback adaptive hierarchical pinning control scheme is proposed. Based on stability theory, several sufficient conditions are established to accomplish lag consensus of multiagent systems in two-layer networks. Eventually, the results are verified using two numerical examples.</p>