According to the structural layout and mechanics characteristic of microsatellite, the FEM was established reasonably. Base on the FEM analysis and its characteristics, the structure of microsatellite was optimization designed. In the optimization process, the optimization model was established with the design variables of aluminum panel thickness, core plate thickness and skeleton thickness, and subjected to stiffness, strength, displacement and size constraints. Then, used the sequential quadratic programming method for optimization analysis. The results of the optimization demonstrates that the weight of structure loss significantly, and the whole structure weight of the microsatellite loss 11%.Meanwhile, the iterative times of the optimization process is few, so it is very Meaningful and useful for actual project application.