With the continuous development and progress of wireless self-organizing network communication technology, how to carry out long-distance cooperative control of multiple intelligences under the framework of an air–ground integrated wireless high-mobility self-organizing network has become a hot and difficult topic that needs to be solved urgently. This paper takes the air–ground integrated wireless high-mobility self-organizing network system as the basic framework and focuses on solving the long-distance cooperative fault-tolerant control of multi-intelligent bodies and the topological stability of a wireless mobile self-organizing network. To solve the above problems, a direct neural network with a robust adaptive fault-tolerant controller is designed in this paper. By constructing a symmetric population neural network model and combining it with the Lyapunov stabilization criterion, the system feedback matrix K has the ability of autonomous adaptive learning, and symmetrically distorts, rotates, or scales the training data to instantly adjust the system’s fault-tolerant corrections and adaptive adjusting factors to resist the unknown disturbances and faults, to achieve the goals of multi-intelligent body stable control and the stable operation of a wireless high-mobility self-organizing network topology. Simulation results show that with the feedback adjustment of the multi-system under the designed controller, the multi-system as a whole has good fault-tolerant performance and autonomous learning approximation performance, and the tracking error asymptotically converges to zero. The experimental results show that the multi-flight subsystems fly stably, the air–ground integrated wireless high-mobility self-organizing network topology has good stability performance, and the maximum relative improvement of the topology stability performance is 50%.