3D imaging technology is widely used in autopilot, aviation mission and military field. Imaging systems with different technical regimes have different advantages. Among them, three-dimensional imaging technology based on multi-pixel photon counter (MPPC) has broad development potential because of its advantages of fast imaging speed and sensitivity to extremely weak light. However, due to the immature development of MPPC array, the detection level of weak light 3D imaging based on MPPC array is limited. In this paper, a three-dimensional imaging system is developed by using the 32×32 scale MPPC array S15013 series two-dimensional photon counting image sensor developed by Hamamatsu company of Japan. Each pixel of the sensor is composed of 12 single photon avalanche diodes in parallel, and its total detection pixels are more than 1 K. Based on the system, the effects of threshold voltage, lens aperture and other parameters on the three-dimensional imaging detection results are analyzed, the detection sensitivity and accuracy of the system are tested, and the three-dimensional imaging detection test is carried out for the simulated target 37 m away. The experimental results show that under the dark condition of echo photons of about 1.98 photons/pixel, the ranging accuracy of the target area reaches 0.268 m, and the three-dimensional structure characteristics are obvious, which is close to the detection level of single photon imaging.