To enhance the effectiveness of the FMS (flexible manufacturing system), it is necessary for the manufacturing control system to be upgraded by integrating the cyber and the physical manufacturing systems. Using the CPPS (Cyber-Physical Production System) concept, this study proposes a 4-stage vertical integration and control framework for an aircraft parts manufacturing plant. In the proposed framework, the process controller prepares the operations schedule for processing work orders generated from the APS (advanced planning & scheduling) system. The scheduled operations and the related control commands are assigned to equipments by the dispatcher of the line controller. The line monitor is responsible for monitoring the overall status of the FMS including work orders and equipments. Finally the process monitor uses the simulation model to check the performance of the production plan using real time plant status data. The W-FMCS (Wing rib-Flexible Manufacturing Control & Simulation) are developed to implement the proposed 4-stage CPPS based FMS control architecture. The effectiveness of the proposed control architecture is examined by the real plant’s operational data such as utilization and throughput. The performance improvement examined shows the usefulness of the framework in managing the smart factory’s operation by providing a practical approach to integrate cyber and physical production systems.