Position sensitive micro-channel plate (MCP) is a kind of high sensitivity detector with low noise, Combined with advanced time-correlated single photon imaging technique (TCSPC) could make a moderate aperture system be sensitive to only one single arriving photon. In this paper, a theoretical model of photon counting imaging with Position sensitive MCP was established and the factor of laser power affecting the detect possibility was analyzed. the three-dimensional point clouds data are generated using Monte Carlo simulation and the typical space target could be reconstructed three-dimensionally. Through the all-chain simulation model the comprehensive performance of the MCP based active three-dimensional imaging system could be analyzed from viewpoint of detection probability, ranging accuracy and signal to noise ratio etc. The application of the position sensitive MCP based active three-dimensional imaging system for long range space objects is verified in simulation condition. The results shows that only a single pulse energy of tens of mico-Joule is needed for the positive sensitive MCP based active three-dimensional imaging system to image the target at the hundreds of kilometers. the counting rate could reach 10(6) counts/s. And the ranging accuracy of this active three-dimensional imaging system for the objects at 300 kilometers could reach 0.1228meters by simulating with 50 mico-Joule single pulse power.