An improved fuzzy neural network (FNN)/proportion integration differentiation (PID) compound control scheme based on variable universe and back-propagation (BP) algorithms is proposed to improve the ability of disturbance rejection of a three-axis inertially stabilized platform (ISP) for aerial remote sensing applications. In the design of improved FNN/PID compound controller, the variable universe method is firstly used for the design of the fuzzy/PID compound controller; then, the BP algorithm is utilized to finely tune the controller parameters online. In this way, the desired performances with good ability of disturbance rejection and high stabilization accuracy are obtained for the aerial ISP. The simulations and experiments are, respectively, carried out to validate the improved FNN/PID compound control method. The results show that the improved FNN/PID compound control scheme has the excellent capability in disturbance rejection, by which the ISP’s stabilization accuracy under dynamic disturbance is improved significantly.