A photon counter model was established to analyze theoretically and measure actually the effect of dead time of the photon counter in a micro-pulse lidar. A correct method for the influence of photon-counting on micro-pulse lidar signals was proposed. The Markov chain was used to theoretically describe the detection process of the photon counter in the micro-pulse lidar theoretically. Then, the influence of dead time on photon counting was calculated based on MATLAB, and the transient morphological changes of the results due to the dead time of photon counting were described. After the theoretical analysis and computer simulation, a photon counting platform based on micro- pulse lidar was performed to illustrate the effect of the dead time on counting photons. Finally, the effect of the dead time was measured under different light intensities, and the correction method of the micro-pulse lidar signal was given. A correction experiment was carried out based on the proposed method. The results show that the effect of photon counting on the scattering light has been reduced by 50%. It concludes that the proposed method has well explained the signal shapes of small targets and achieves the correction of the detection results of photon counts.