A continuous wave (CW) radar sensor system with active transponders is designed for Structural Health Monitoring (SHM) to accurately measure the structures' vibration while rejecting clutters reflected from the surrounding environment. The radar sensor, designed with a coherent heterodyne architecture, transmits a single-tone 2.4 GHz signal and receives a returning signal at 3.3 GHz, thus rejecting the backscattered clutters at 2.4 GHz. The active transponder was designed to convert the received 2.4 GHz signal up to 3.3 GHz and transmits a 900 MHz reference to synchronize the radar sensor. The proposed radar with active transponders was tested in lab environment to successfully capture vibration movements from 4.1 m with SNR over 35 dB. Experiments also showed that the radar sensor can isolate the target motion from the interferences from surrounding shaking bodies and sinusoidal phantom motions.