The invention discloses a frequency changing method of digital middle-frequency signals used in a repeater station system, which comprises two steps of an up frequency changing process and a down frequency changing process: in the down frequency changing process, the middle-frequency signals after digital analog conversion are processed by digital wave filtering processes such as an extraction process, a bandpass compensation, a signal shaping process, etc. after a digital frequency mixing process, the middle-frequency signals can be moved to a zero middle-frequency, a digital signal with the high speed rate can extracted as two-channel quadrature digital baseband I, Q signal with a low speed rate; in the up frequency changing process, the digital baseband I, Q signals acquired from the down frequency changing process are processed by an interpolation filtering process, then processed by I, Q modulation process and a secondary frequency mixing process, and the signals can be processed by a gain adjustment and control, finally high speed digital middle-frequency signals are outputted. Correspondingly, the invention also discloses a frequency changing system thereof. The invention can be achieved by using PLC units such as FPGA, CPLD, EPLD and DSP, etc., which can improve the integration degree of repeater station equipment; meanwhile, an ASIC chip is removed to decrease heating capacity and to improve the reliability.