A lOOkV/IOOA High Vo ltage Power Supply (HVPS), which will provide the energy for 4MW ion source of the neutral beam injection (NBI), has been developed in Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP). The power supply is based on the technology of pulse step module (PSM)[l] which consists of many DC chopper module with the same configuration. NBI requires that the power supply can provide fast turn-on and turn-off voltage for sustaining the beam current. Therefore the control of the HVPS is important parts of the NBI power supply systems. The HVPS' control system consists of cPCI computer which performs the fast real time control within microseconds, monitor PC which supervises the state of power supply, local controller inside each module DC chopper module, and current and voltage measurement.The HVPS and its control system has completed in the end of last year. This paper will present the details design, manufacturing, integration and commissioning of the control system, and some related test results for the power supply is also be presented.