This paper established an accurate thin-layer element equivalent model describing the dynamic characteristics of bolt connection joint surfaces, and reverse optimized the material parameters of the thin-layer element based on experimental results. Utilizing finite element methods, the stiffness influence law of preload force on the sub-flange edge of the connected component was obtained, taking into account bolt preload and contact friction at the joint surface, meanwhile, based on finite element simulation results, it was found that with the increase of preload force, the stiffness of the bolt connection structure exhibited a nonlinear “softening” characteristic. For the material parameters of the thin-layer element, initial values were determined through theoretical calculations, followed by modal experimental research on the bolt-flange connection cylindrical shell structure to obtain the dynamic parameters of the structure. Finally, a surrogate model combined with genetic algorithms was adopted to optimize the material parameters of the thin-layer element, and compared with experimental results, demonstrating that the errors of the first 5 orders were all within 5%, validating the effectiveness of the thin-layer element modeling and parameter identification methods.