This thesis deals with the design and implementation issues for the Cyber-Physical System based production control system in an aircraft parts manufacturing plant, WFMS (Wing rib Flexible Manufacturing System). Digital 3D models of the wing rib manufacturing equipment and material handling devices and so forth are devised and built into a cyber plant. And also the flows of control information and products within the WFMS are described with a commercial discrete event simulation engine. Using several relevant performance statistics from the 3D simulation runs, the validity and efficiency of a production scenario can be confirmed prior to actual production. The 3D animation model also serves as a digital twin of physical WFMS by synchronizing the status of the digital model with the status of the physical shop floor at every occurring event. On the basis of the digital 3D model, a 4-stage vertical integrated control framework is proposed including process controller(PC), process monitor(PM), line monitor(LM), line controller(LC) modules. In the proposed framework, the PC prepares the operation schedule to process the work orders downloaded from upper-level planning systems such as enterprise resource planning(ERP) or advanced planning system(APS). Data about the scheduled operations with control commands are compiled and transmitted to relevant equipment by the dispatcher of the LC. The LM is responsible for monitoring the overall status of the FMS including work orders and equipment. Finally, the PM 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 CPS based FMS control architecture. W-FMCS is implemented and operated at a Korean aircraft parts manufacturing factory. The effectiveness of the proposed control architecture is examined in terms of utilization, lead-time, work-in-progress inventory level, and throughput.