The invention discloses a frequency conversion compensating microwave frequency transmission system and method. A phase pre-compensated microwave transmission signal is loaded into a laser signal, thelaser signal is transmitted to a remote end through utilization of an optical fiber, and the remote end restores the laser signal into a frequency signal synchronous with a microwave reference frequency signal of a local end through detection. According to a specific process, after a local signal is transmitted to the remote end, frequency conversion is carried out on a detection signal of the remote end, the detection signal is returned to the local end, a return signal comprises phase noise imported into an optical fiber link; the return signal and the local transmission signal are respectively mixed with the local reference signal, comparison is carried out to acquire pre-compensation quantity and a crystal oscillator generating the transmission signal is controlled according to the compensation quantity, so phase compensation of high precision frequency transmission is finished. Compared with existing frequency transmission, the method mainly has the advantages that frequencies ofthe signals transmitted by the local end and returned by the remote end are different, the phase interference of strong signals of stations at the two ends for detected and received weak signals is avoided, and the frequency transmission stability is further improved.