In the field of modern aviation, the demand for civil aircraft design is growing rapidly and the granularity is continuously refined. Civil aircraft design has gradually become a large-scale, multi-disciplinary and complex system engineering with multi-disciplinary integration. In recent years, model-based systems engineering has gradually become a mainstream idea in civil aircraft design and has been widely used in the field of civil aircraft design. However, when the MBSE methodology analyzes the logical relationship between subsystem-level and component-level design activities, it is often simply defined as a finish-start relationship. This relationship cannot effectively describe the actual logical relationship between design activities, which in turn leads to problems such as extending the civil aircraft design cycle and increasing design costs. Aiming to solve the problem, this study firstly analyzes the generalized precedence relations between design activities. Secondly, the corresponding mathematical model was established. Finally, the Strength Pareto Evolutionary Algorithm 2 (SPEA2) is improved and be verified the effectiveness in the case of flight control system design.