In order to meet the urgent demand for novel zero-expansion materials and ultra-stable structures in space gravitational wave detection, it is necessary to develop an ultra-stable structural spacecraft system. This paper focuses on the research of the optimization of the core ultra-stable structure design of spacecraft, proposing a cross-scale parameterized model of structural deformation response and a multi-objective optimization method. By satisfying the prerequisites of mass and fundamental frequency, this paper breaks through the limitations of current linear analysis methods, and the overall thermal deformation of nonlinear material composite structures is optimized by modifying structural parameters.