Range accuracy is one of the important parameters for evaluating the performance of the pulsed laser ranging system. In this paper, the range accuracy of the photon pulsed heterodyne detection system with Geiger-mode avalanche photodiode (GM-APD) is investigated. Based on the heterodyne principle and statistical detection theory of photon counting, the range accuracy model is established. The factors that influence the range accuracy, inculding pulse width, echo intensity, local oscillator (LO) intensity, noise, echo position, and beat frequency, are discussed. The results show that these six factors have significant influence on the range accuracy when the echo intensity is extremely weak. In the case that the primary electrons of the echo signal are beyond 4, the pulse width and echo intensity are the main factors. It is also shown that the stronger echo intensity, the narrower pulse width, the lower noise, the larger echo position, and the less beat frequency, the higher range accuracy in a pulsed photon heterodyne detection system based on GM-APD.