Multi-beam single-photon radar has important applications in fields such as earth surveying and long-range imaging, and multi-channel timing measurement technology significantly determines the performance of the entire system. Therefore, we propose a parallel measurement method of multi-channel time-to-digital conversion based on clock phase shifting method. Through a single Xilinx Artix-7 series field-programmable gate array chip, the method can realize the simultaneous timing measurement of 100 channels single-photon signal. The timing resolution of 1.0 ns, the measurement accuracy is 360 ps, and the range of 65 μs. Based on the device, the multi-channel single-photon echo signal measurement are remarked on the advantages as high stability, low power consumption, high speed, and compact structure, which meets the timing requirements of the multi-beam single-photon radar.