This paper reports the model-based functional analysis and architecture design for the auto flight control system on commercial aircraft. The system engineering process develops functional models that can define and validate the system functions. The functional flow is logically dynamic upon changes in operational states, humanmachine interaction and external environment. Its static and dynamic characteristics are systematically studied including external actors, application cases, functional logics, interactive sequence and state shifting. The logical architecture and interfaces are also generated, and relevant requirements are allocated accordingly as development references of physical architecture and implementation design. The study examines availability and integrity of flight guidance, auto thrust, auto landing, crew warning and alerts functions and improves the design requirements.