This paper presents a new kind of electro-discharge machining (EDM) software computer numerical control (SoftCNC) system which is based on RTLinux platform and Finite State Machine (FSM) method. An EDM SoftCNC function model is given and the structure of SoftCNC based on the function model is proposed. The Binary FSM (Motion FSM and control FSM) model of the whole system is also proposed. To simplify complexities, the system FSM is decomposed to a set of FSMs. The motion decision-making FSM which is the dispatcher of motion tasks is designed. The auto task FSM and interpolate algorithm FSM are proposed. In control FSM, the control signal generator-decoder model is proposed, as well as the auto decision FSM is fabricated. Three abstract layers: function abstract layer, communication abstract layer and hardware abstract layer are designed to enhance enclosure and porting of SoftCNC. Run on MD21 machine, the performance implies that the system is stable, reliable and with low-latency.