Photomultiplier tubes (PMT) have unique advantages in photon-counting radar 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 be stacking between different pulses. When using the fixed threshold method to identify the photon 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 setting of photon event identification threshold on the photon event detection probability, a new PMT photon detection theoretical model was proposed and simplified according to the actual application scenarios. The applicability of the simplified model was verified by Monte Carlo simulation. The correlation characteristics of the new model in photon counting distance measurement are analyzed. A photon counting radar system is built, compared with GM-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 ranging applications. The experiment also proves that the new model is more consistent with the photon event detection probability distribution 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 radar.