A multiple-objective evolutionary algorithm (MOEA) with a new Decision Making (DM) scheme for MOD of conceptual missile shapes was presented, which is contrived to determine suitable tradeoffs from Pareto optimal set using interactive preference articulation. There are two objective functions, to maximize ratio of lift to drag and to minimize radar cross-section (RCS) value. 3D computational electromagnetic solver was used to evaluate RCS, electromagnetic performance. 3D Navier-Stokes flow solver was adopted to evaluate aerodynamic performance. A flight mechanics solver was used to analyze the stability of the missile. Based on the MOEA, a synergetic optimization of missile shapes for aerodynamic and radar cross-section performance is completed. The results show that the proposed approach can be used in more complex optimization case of flight vehicles.