C/SiC material is a kind of poor thermal conductor and has important potential applications in the field of thermal insulation. The finite element model modification method of C/SiC structural parts is studied in this paper. Based on the elastic theory in thermal environment, the stress-strain relationship of anisotropic materials is deduced, and the system functional of C/SiC composite laminates under high heat flux conditions is given. The Hamiltonian formula of composite laminates is derived, and the kinetic energy and potential energy of composite laminates are calculated. The C/SiC typical component-level structure finite element model for calculating thermal environment of structural dynamics is established. Then, the dynamic finite element model of C/SiC composite structure considering temperature effect is established. Finally, a method of modifying the C/SiC composite structure model based on the multi-level idea was proposed. With the minimization of the modal frequency difference as the correction objective, and the mechanical and thermal parameters of the composite as the correction variables, the hierarchical model was modified. The model modification results show that the proposed method has good correction effect and can accurately correct the composite material parameters and boundary conditions in the thermal environment of the structure.