The invention provides a space-borne S-band and X-band link reconfigurable tracking, telemetry and command transponder. One receiving channel is used for performing down-conversion on S-band and X-band two uplink signals, combining the two uplink signals into one path of signal at middle frequency, performing AGC amplification filtering, and then sending the processed signals to a digital processing circuit, and then the digital processing circuit captures and demodulates remote-control signals and ranging signals by utilizing the received signals; meanwhile, digital processing software controls local frequency of the receiving channel and an emission channel according to S-band and X-band coincidence frequency calculation, and sends telemetered signals and forward ranging signals to the emission channel; and meanwhile, local frequency point setting is performed by software calculation, one receiving and transmitting channel is utilized to achieve uplink and downlink reconfiguration in an S band and an X band, so that the weight, the size and the power consumption of products are reduced, tracking, telemetry and command requirements of a moon relay satellite are met, the S band and the X band are utilized to complete tracking and telemetry of a satellite under a uniform carrier wave system, an uplink and downlink reconfiguration function is achieved, and uplink and downlink signal frequency is changed according to commands, so that forward and backward link requirements of a moon rover are met.