With the continuous development of the times, hypersonic technology has become one of the focuses of current aviation research. The process of multi-body separation/load release is ubiquitous. In the process, the lumped uncertainties, including parameter uncertainty, unmodeled dynamics, and unknown disturbances, makes the design of the controller difficult. In order to maintain the stability of the lateral motion of the aircraft during the separation process, a backstepping control method based on command filter and neural network is proposed. A dual command filter to obtain the derivative of the differential signal between the virtual input variable and the virtual control law; Traditional neural network-based backstepping controller requires multiple neural network, and this kind of controller will lead to a more complex and fragile system. Our method requires only a single neural network to approximate matched uncertainties, effectively addressing the complexity and fragility issues inherent in traditional multi-neural-network-based backstepping controllers. Finally, the effectiveness of the designed separation control method is confirmed by simulation.