This paper proposes a RISE-based cooperative control of uncertain multi-agent system with exogenous disturbances. First, we introduce the second order model with disturbance for agent. The network topology among agents is undirected and connected, and information of reference is allowed to be available to at least one agent. Second, we propose the control law consists of graph theory, consensus algorithm and RISE. Graph theory and consensus algorithm are utilized to converge the states of agents to reference value, and RISE is utilized to suppress the disturbance. Then, we show the proposed control law guarantees the agents achieve synchronization, and derive the condition to achieve the control objective. Finally, simulation results show the effectiveness of the proposed control law.