Photomultiplier tubes (PMT) have single photon level sensitivity, low dark count, low after pulse probability, and are widely used in photon-counting lidar in visible spectrum. PMT has no photon detection dead time, for every photon it responds to, it sends out a electron flow pulse, these pulses of electron flow have the po·tential to pile up into larger pulses. When using threshold identification method to identify photon-events, stacked pulse will introduce additional pulse walking error, in the practical application of laser ranging, will directly affect the ranging precision of photon-counting ranging method. Considering the influence of pulse pile-up, a new theoretical model of PMT photon detection was established to describe the influence of pulse pile-up on the detection probability of photon-events by analyzing the relationship between the detection time of photon and the identification time of the PMT final output photon-events. Through Monte Carlo simulation, the relationship among the ranging walking error, ranging accuracy, incident laser pulse width, PMT output electron flow pulse width and photon-events identification threshold is obtained. In order to verify the correctness of the theory, a PMT-based photon-counting lidar system is built. The comparison experiment with GM-APD proves that the influence of pulse pile-up on PMT photon-counting ranging method can not be ignored, and the experimental results are in good agreement with the theoretical model. The PMT photon detection model based on pulse pile-up can guide the design of PMT photon-counting radar and improve the ranging accuracy and precision of the ranging system.