The design and development for aircraft is a complex system engineering process involving multi-disciplinary, multi-objective and multi-constraints, tightly coupled systems, large number of participants, and complex design information. Traditional R&D methods such as document-centric requirements management show some difficulties, and new aircraft design and R&D methods need to be explored urgently. In this paper, with aileron and its control system as the research object, a model-based system engineering (abbreviated as MBSE)method is explored and studied. Using Dassault MBSE methodology-MMS(Modeling Methodology for Systems), the aileron and its control system are analyzed from perspectives of mission, service, function and component, and then the system is defined completely. With Dassault 3D Experience platform and RFLP system engineering architecture, we have finished requirements development, functional analysis and logical architecture design of the aileron and its control system. We have carried out the correlative traceability of requirements, functions, logical architecture, system simulation, physical design and other models. And finally the effective application of R&D technology with Dassault MBSE methodology as the core has been realized.