Aiming at the accuracy, real-time and synchronicity requirements of Terahertz human security inspection instrument for data acquisition, the problems of amplitude nonuniform error, clock jitter and sampling trigger jitter of the acquisition system are analyzed, and the acquisition system structure of active Terahertz human security inspection instrument is proposed. In order to determine the allowable range of clock jitter in the acquisition system, a high-precision programmable time-delay clock tree network structure is designed to realize the output of seven-channel sampling clock, sampling trigger signal and synchronous clock with homology, low jitter and consistent phase. Finally, the system test scheme is introduced. Experimental results show that under the same test conditions, the clock tree mechanism of terahertz human security inspection acquisition system within -40~ 40MHZ band, I and Q signals were collected good orthogonality, waveform distortion and the amplitude are equal, the second harmonic signal spectrum is below -40dB. Compared with the traditional system, the harmonic suppression reduced by more than 10dB, can be used in the field of terahertz human security inspection.