To investigate the formation-containment problem of discrete-time heterogeneous multi-agent systems, the formation-containment protocols with time-varying delay are presented. Firstly, based on reasonable hypothesises, by model transformation and state space decomposition, the problem of formation-containment is transformed into stability problem of subsystems. By using the Lyapunov-Krasovskii function, the sufficient conditions that guarantee the effectiveness of the proposed protocols are presented in the form of LMIs, and it is pointed out that the number of LMIs is independent of that of agents. Then, the formation reference function is also described in detail, and the proof illustrates that the formation reference function is not affected by time-varying delay. Finally, the simulation results demonstrate the effectiveness of the designed protocols.