The present invention discloses the method and system for synchronizing the transceiver and the instrument. The instrument includes signal source, and the transceiver includes voltage controlled vibrator to generate the local vibration signal and frequency mixer. The method includes: A. for the signal source to generate one first monotonic signal and to send the signal to the transceiver; B. for the transceiver to receive the first monotonic signal, to mix the first monotonic signal and the local vibration signal to generate the second monotonic signal; C. to measure the frequency of the second monotonic signal and to obtain local vibrator drift frequency through calculation with certain formula; and D. to regulate the voltage to the voltage controlled vibrator to correct the frequency drift of the said transceiver. The present invention can synchronize the transceiver and the instrument without need of increasing any hardware interface, and has low cost and wide application range.