This study has constructed a fully automated multidisciplinary and many-objective evolutionary design optimization system independent of computer environments to evaluate objective functions; the research applied it to a geometric design problem of a flyback booster for next-generation space transportation. In optimization involving objective functions to appraise the aero-/structural-dynamic performance with high fidelity, spatial discretization hinders the overall automation. This research has facilitated an efficient optimal design by wholly automating high-fidelity assessments, which designers had to implement manually, and has accomplished optimizations that directly contribute to real-world design problems. Moreover, this study would accumulate design knowledge for space transportation that the market is reviving. The total automated system yielded the embedding of geometric trait lines to ensure the discretization even for large curvature surfaces; the system innovated a robust automatic error-checking mechanism in the system’s preprocess. Consequently, the entirely automatized optimization procured nondominated solution sets for more precise data analyses in a pragmatic execution period. Design informatics, a framework combining optimization and data analysis, functioned usefully in real-world design on flyback-booster geometry by materializing smooth deriving and verifying a design hypothesis; eventually, the research gained a new design principle.