This research focuses on intelligent missiles that possess advanced intelligent features such as variable shapes, adjustable propulsion, and intelligent planning. The trajectory optimization of such missiles essentially constitutes a multidisciplinary optimization problem involving aerodynamics, propulsion, structure, and trajectory. Its core objective is to identify the optimal variation strategy of aerodynamic shape, propulsion adjustments, and trajectory-control laws under various constraints to optimize specific flight-performance indicators. This research investigates the intelligent guidance design of the novel missiles from three perspectives: the trajectory optimization problem modeling, the construction of the optimization solution method, and the application of the proposed method. From the aforementioned three aspects, an integrated trajectory optimization method is proposed that is suitable for the intelligent missiles, considering aerodynamics, propulsion, and trajectory disciplines simultaneously. The method fully exploits the intelligent characteristics of the intelligent missile, offering a guidance approach for the intelligent missiles, enhancing the performance of the intelligent missiles, and providing a reference for the trajectory design of various types of the intelligent missiles.