In order to reduce the weight of the wing, distribute materials reasonably and improve utilization rate of materials, Two-Step optimization method was proposed for flap structure optimization Design. Taking the conceptual design of flap guide as research object, top-layer and low-layer optimization design as two basic events were analyzed by complex optimization design problem. The top-layer was topology optimization that determined web stiffener forms and low-layer was size optimization that determined thickness distributing of flap guide. During this two-step optimization, this process determined the best structure forms base on minimize structure weight．The results of the calculative examples indicate that the method presented in this paper is feasible and correct, has a significant value in accelerating the engineer realization of the structure optimization．