With the increase of welding thickness, Friction stir welding equipment (FSW) with traditional milling machine structure could not meet the requirements of stiffness which to support the huge axis load. Therefore, a FSW with serial-parallel mechanism based on 3-PRS platform was proposed. In order to complete real-time control and the actual and virtual axis control of the equipment, the positive solution and inverse solution (based on Newton-Euler method) of the FSW are analyzed. Then, based on the PA system, the open CNC of the equipment is designed, and the inverse kinematics and the numerical positive kinematics based on Newton-Euler method are embedded into the interpolation of NC system. According to the demand of the equipment, human-machiner interface (HMI) is developed to display the positions of actual and virtual axis for the equipment, and compiler and interpolation are designed. At the same time, online real-time 3D motion simulation is designed, space pose of spindle and whole for the equipment are deduced. In the paper, design method of CNC based on the serial-parallel mechanism is provided.