The invention relates to a terahertz radar detection system based on a Zynq platform and a method thereof. The system comprises a terahertz transmitting and receiving device, a Zynq processing platform, a control system, an upper computer and a two-dimensional motor. The terahertz transmitting and receiving device is in communication connection with the input end of the Zynq processing platform; the output end of the Zynq processing platform is in communication connection with the input end of the control system and the upper computer; and the output end of the control system is in communication connection with the control two-dimensional motor and the terahertz transmitting and receiving device. According to the terahertz multi-channel radar detection system based on the Zynq platform and the method thereof, the frequency synthesis and modulation waveform generation assembly is controlled by the control system, linear frequency modulation signals of continuous waves, narrow bands and wide bands are generated according to different detection modes, the Zynq processing platform serves as a core processing unit, so that the functions of multi-channel intermediate frequency echo data processing, self-calibration, target searching, high-resolution imaging and the like can be realized.