A consensus control method based on distributed observer is proposed for a class of multi-agent systems with actuator faults and external disturbances. This method estimates the state and fault information of the system through a distributed observer, and designs a consensus control protocol, which can estimate the state and fault of the system under the condition of actuator failure and external disturbance, and realize the fault-tolerant consensus of the system. Firstly, based on the output information of the agent subsystem and the state estimation information of the adjacent subsystems, a distributed fault observer is constructed, and a new Lyapunov function is designed to obtain a sufficient condition for the global dynamic stability error convergence of the system. It is proved that the gain matrix of the designed observer can effectively estimate the system state and fault information. Secondly, based on the fault estimation results, a consensus control protocol based on output feedback is proposed, which can effectively compensate for actuator faults and suppress the influence of external disturbances on system stability. Finally, the feasibility and effectiveness of the proposed method are verified by the simulation experiment of the UAV system. The results show that the designed control method can achieve fast convergence and fault-tolerant consistency of the system, and has good robustness.