Aviation systems are characterized by the synergic interaction between their components from different technological domains. These interactions enable the system to achieve more functionalities than the sum of the functionalities of its components considered independently. Recently, Model-Based Systems Engineering (MBSE) is an interdisciplinary approach for handling complexity during product development. However, the generic methodology guides the engineers toward a specific model-based system design is lacking. Besides, it still calls for efforts on investing in a specific case study. To overcomes the gaps, this paper proposes a generic model-based system engineering methodology to conduct the mission and system-specific design for aviation systems development.