The invention discloses a frequency transmission system based on digital compensation systems, and a transmission method of the frequency transmission system. In combination with an intensive wavelength division multiplexing transmission device, an optical frequency locking device and the digital compensation systems, a mode locking laser receiving device is locked on a frequency reference signal transmitted at a local end by utilizing the optical frequency locking device at a far end, a frequency reference signal for bearing the practical noise information of an optical fiber link is recovered and is transmitted to the local end by utilizing the intensive wavelength division multiplexing transmission device, the local end digital compensation system is used for transmitting the obtained noise information to the far end again through the intensive wavelength division multiplexing transmission device, the far end digital compensation system is used for compensating the frequency reference signal at the far end according to the received noise information, and thus the stable frequency reference signal locked with a quantum frequency source is obtained. By the method disclosed by the invention, higher frequency transmission stability can be achieved in the long-distance and high-precision optical fiber frequency transmission process.