The invention relates to a multi-frequency multi-base high-frequency ground wave radar system and an operating method thereof. The multi-frequency multi-base high-frequency ground wave radar system comprises an analog extension, a digital extension, an ultra-high-stability time frequency standard device, a power amplifier, a transmitting antenna, a receiving antenna and a GPS (global position system) antenna. The analog extension comprises a frequency synthesizer, an analog amplification filtering component, an analog frequency multiplier and a multi-channel analog receiving front end, and the digital extension comprises a multi-channel data acquisition and processing board card, a synchronization control board card and an industrial control computer. The frequency synthesizer adopts a digital up-conversion scheme; the analog receiving front end adopts a multi-stage broadband program-controlled tracking and filtering scheme with no need for frequency mixing; data acquisition adopts a radio-frequency direct sampling and digital down-conversion scheme; and the time frequency standard is provided by a GPS tame low-phase-noise and ultra-high-stability crystal oscillator. The multi-frequency multi-base high-frequency ground wave radar system has the following advantages that the all-digital transmission and reception technology is adopted, and the system has good universality and scalability; and the radar waveform and time sequence are flexible and controllable, and the time-sharing, multi-frequency and single-base or multi-base detection can be realized.