This paper presents a new kind of multi-axis electro-discharge machining (EDM) computer numerical control (CNC) system which is based on RT-Linux platform. Binary kernel structure of EDM CNC System is proposed to handle real-time task and time-sharing task separately. The system is divided into three parts: CNC kernel module, CNC driver module and CNC user module. CNC kernel module implements CNC control function in of the software system, and implements the move control to the NC machine. CNC driver module is just as device driver level. CNC user module is user manage procedure. The experiment of rimed turbine blisk validates the performance of the system. The performance implied that the system is real-time, stable and reliable.