To realize the automation process for Pin implanting of X-cor sandwich structure, a hardware architecture of CNC based on open control system was proposed in which a Programmable Multi-axes Controller (PMAC) was adopted as the key unit for motion control and the accessory card for on-off control. The time based control mode is applied to realize synchronization of motion control and on-off control and to improve the real-time effort of the main tasks that closely related to the Pin implanting process. In addition, the device driver for PMAC, a user graphical interface as well as numerical control program interpretation module were also designed and the whole system is applied to the core material manufacturing process of X-cor sandwich structure.