The Flap system is the significant system, and the flap electronic control unit is the core component. The double-V development process of SAE ARP4754A based on the requirements is the standard which is should followed by the civil aircraft. The research focuses on the flap electronic control unit is the core component, on the beginning, the design inputs in terms of function requirements， performance requirements and interface requirements are explained；Then, the paper surmises the Flap system architecture and working principle for civil aircraft, analyses the control logic for system's normal working and fault protection, uses Simulink to model and simulate, and build user interface by GUI. This study can be provide as a reference for the civil aircraft Flap control system design.