In order to meet the needs of the wide range of frequency and changeable voltage, and the combination of multi-frequency and multi-power in water process, a new frequency converting electromagnetic water treatment control system is developed. The frequency ranged from 1Hz to 1MHz is produced with the DDS pulse chip controlled by MCU, which guarantees that the range of frequency converting is wider. By using the switch circuit and MOSFET, the amplifier circuit is designed. The circuit and CNC power enlarge the output electromagnetic pulse power adjustable range. The software developed with LabVIEW makes frequency work under three kinds of frequency converting modes. And it also can make voltage run under the mode of voltage selecting and user-defined voltage converting. The designs improve the applicability of frequency converting electromagnetic water treatment (FCEWT) system.