We demonstrate a photon counting three-dimensional radar system based on a micro-channel plate (MCP) detector with a position-sensitive anode. The system is mainly composed of a laser device, a photon counting imaging detector and readout electronics. The probe laser is divided into two channels. One is used to trigger the start signal, and another irradiates the sample. The reflected light enters into the MCP, and it generates the trigger stop signal. The flight time of the laser pulse is obtained through a constant fraction discriminator(CFD) and a time-to-digital converter (TDC). The time resolution can reach the nanosecond level. The distance information of targets at different distances was measured using this system. The results show that the depth resolution of the system is centimeter level. The performance of the system is demonstrated by imaging of a resolution target and a space object. © 2022 SPIE