Photomultiplier tubes (PMT) have unique advantages in photon-counting LIDAR applications due to its photon-level sensitivity and lack of photon detection dead time. However, the output pulse height of PMT responds to the single photon follows the Gaussian random distribution, and there may produce pile up between different pulses. When using the fixed threshold method to identify the photo-events, the traditional single photon model can not accurately describe the photon detection process of PMT. By analyzing the influence of PMT output pulse height distribution, pulse pile up and the amplitude of photo-event discrimination threshold on the photo-events detection probability, a new PMT photon detection theoretical model was built, and the mode was simplified according to the practical application scene. The applicability of the simplified model was verified by Monte Carlo simulation. The correlation characteristics of the new model in photon-counting ranging are analyzed. A photon-counting LIDAR system is built, compared with Geiger mode APD, the PMT photon detection model has a slight loss of photon detection probability, but it has a smaller ranging walking error and higher ranging accuracy in photon-counting ranging applications. The experiment also proves that the new model is more consistent with the photo-event detection probability of PMT than the traditional single photon detection model. The new model has important guiding significance for the system design and theoretical analysis of PMT photon-counting LIDAR.