The invention discloses an active pilot frequency transceiver microwave radar system facing large-scale structural deformation monitoring. The signal send from RF signal source S0 and S1 is divided into two channels: S0t, S0ref and S1t, S1ref. The S0t amplified by a power amplifier gets through A group of antennas to become the S0re after passing through a circulator; the S1t amplified by the power amplifier gets through A group of antennas to become the S1re after passing through the circulator. The S0ref and the S1re in a mixer are mixed to generate reference signal; the S1ref and the S0re in the mixer are mixed to generate SM, the SM is frequency-modulated by a demodulator and passes through B group of antennas, and then is demodulated into measurement signal. Finally comparing phase difference to get variable quantity of space R. Microwave leak and multipath reflection, eliminated by the pilot frequency, between the antennas are transmitted and received by the pilot frequency transceiver microwave radar system, A group of antennas and B group of antennas do not interfere with each other even they are close as long as the demodulator and carrier frequency of the demodulator and frequency of the two RF Generators are not in one frequency band.