For the flight control problem occurred in 3-DOF Helicopter System, reference adaptive inverse control scheme based on Fuzzy Neural Network model is designed. Firstly, fuzzy inference process of identifier and controller is achieved by using the network structure. Meanwhile, the neural network connection weights are used to express parameters of fuzzy inference. Then, back-propagation algorithm is adopted to amend the network connection weights in order to automatically identify the fuzzy model and adjust its membership functions and parameters, so that the actual system output of adaptive inverse controller control which is adjusted can track the reference model output. Finally, the simulation result of 3-DOF Helicopter System based on the scheme shows that the method is effective and feasible.