In this research, the group consensus problem of second-order heterogeneous multi-agent systems with second-order linear and second-order nonlinear agents is studied. A control protocol with and without input constraint is proposed for the system. Based on graph theory, Lyapunov’s technology, LaSalle’s invariance principle, and other mathematical methods, it is proved that agents in heterogeneous systems can be grouped and reach consensus through control protocols. The conditions for the system to achieve group agreement are proved. Finally, some simulations are carried out to verify the effectiveness of the proposed method.