The invention discloses a treatment control system of high-power and high-frequency electromagnetic anti-scaling water and a control method thereof. The system device comprises a water treatment cavity and a signal generator, wherein the signal generator comprises a signal generation circuit and a power amplifying circuit; a microcontroller is arranged in the signal generation circuit; and the microcontroller is connected with a temperature and flow rate detector, a conductivity and pH detector, a keyboard, an LCD (Liquid Crystal Display) display and a digital frequency synthesizer. The control method of the system adopts three control modes of an automatic frequency regulating mode, a manual frequency setting mode and a frequency circular scanning mode. The invention can ensure that the structure is simple; the effect is good; the frequency and the power of outputting high-frequency signals can be regulated according to specific application conditions; the signal frequency can be manually set and obtained by utilizing the automatic detection of the system as well as output by adopting a sweep frequency mode, therefore, the application environment of the system is amplified; and no secondary pollution is generated.