Joined Wing Aircraft is being in the spotlight due to the fact that it contains so much positive characteristic on Aerodynamics, Structures, and Stability that it can be applied to many application. For these reasons, numerous researches have been performed so far to investigate its flight characteristics especially in the United States. In this paper, an UAV Design Optimization Framework considering both aerodynamics and stability was built, which is able to produce an optimum shape for not only single wing but also joined wing UAV. With this framework, an optimum joined wing and an optimum single wing UAV, which have same wing span and total wing area, were determined. These two optimized UAVs were compared by adopting multidisciplinary analyses. In our case, the optimum joined wing UAV shows better structure performance than the optimum single wing UAV while the aerodynamic and stability performances are similar to each other.