Photomultiplier tube (PMT) features single photon level sensitivity, low dark count, and low afterpulse probability, and are widely used in photon-counting lidar in the visible spectrum. The PMT has no photon detection dead time, for every photon it responds to, it can output an electron flow pulse, these pulses of electron flow are likely to pile up into larger pulses. When using threshold identification method to identify photon-events, the stacked pulse will introduce additional pulse walking error, directly affecting the ranging precision of photon-counting ranging method in the practical application of laser ranging. Considering the influence of pulse pile-up, a new theoretical model of PMT photon detection is 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 comparative experiment with GM-APD proves that the influence of pulse pile-up on PMT photon-counting ranging method cannot be ignored, and that the experimental results are in good agreement with results from 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.