An intelligent control method for a dynamic neural network-based variable cycle engine is provided. By adding a grey relation analysis method-based structure adjustment algorithm to the neural network training algorithm, the neural network structure is adjusted, a dynamic neural network controller is constructed, and thus the intelligent control of the variable cycle engine is realized. A dynamic neural network is trained through the grey relation analysis method-based network structure adjustment algorithm designed by the present invention, and an intelligent controller of the dynamic neural network-based variable cycle engine is constructed. Thus, the problem of coupling between nonlinear multiple variables caused by the increase of control variables of the variable cycle engine and the problem that the traditional control method relies too much on model accuracy are effectively solved.