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Multidisciplinary Design Optimization is a method that developed in decades of years to solve multidisciplinary problems in design.It depends on modern computer technology to explore the interactions between disciplines exhaustively, search for the best plan of the whole system with some optimization algorithm, so it can raise the design speed and the design quality obviously.This paper takes the complex shell cylinder structures for example, optimizes the structures as a whole with multidisciplinary design optimization method.The complex structures contain grid stiffened structure, cone structure and rood beams which are made of composite materials and metal.Building the parameterized finite element models of the three kinds of structures above, including the material definition and the ply orientation of the composite materials, then making them a whole system by defining tie connections, and make sure the whole model is adaptive and stable with the parameters change.Then optimizing the twenty six geometric design parameters with lightening the structure height as target, and limiting structure stiffness, strength, natural frequency, buckling coefficient as restraint.The optimization contains buckling analysis, modal analysis, stiffness and strength analysis.Due to the complexity of this problem, this paper used both global optimization method and local optimization method, multi-island genetic algorithm is used as global optimization method and NLPQL is used as local optimization method.Though the multidisciplinary design optimization, the best structure design parameters are got and the feasibility of the optimization method is proved.