The multi-group formation fault-tolerant control problem for high-order nonlinear multi-agent systems with parameter uncertainties, unknown external disturbances, switching topologies, and non-cooperative targets are investigated in this paper. A fully distributed formation tracking control protocol is proposed based on the total interaction information between subgroups being zero and the neighboring relative information of multi-agent in the subgroups. In addition, an algorithm is proposed to design the parameters of time-varying formation tracking control protocol. At the same time, it does not require knowing the bounds of actuator faults, parameter uncertainties, control inputs of the leaders, and unknown disturbances. Then, it is proved that the designed control protocols can make the high-order nonlinear multi-agent systems accomplish the desired time-varying multi-group formation, and the errors are uniformly asymptotically bounded stable. Finally, the effectiveness of the designed control protocol is demonstrated by simulation examples of three subgroups.