When photon time-of-flight measurement is used, the measurement accuracy will decrease due to the reversal error of time-of-flight measurement. In this paper, a method to correct the reversal error is described in detail. The correction method proposed here included two steps: prior modeling calibration and reversal error correction. Firstly, the function relationship between laser pulse response rate and reversal error was obtained by the calibration method and the reversal error prediction function was established. Then, the reversal error of an original 3D image was calculated by the reversal error prediction function and the 3D image was corrected. Finally, a photon counting 3D imaging lidar system was constructed, in which the Geiger mode Avalanche Photodiode(Gm-APD) was used as a photon detector and the high-speed galvanometer as a scanner. A Time Correlation Single Photon Counting (TCSPC) module was used to mark the arrival time of each photon event. The original 3D image and laser pulse response rate were acquired by the arrival time distribution of photon events. In performance evaluation test, the mean square error of ranging results is improved from 33.2 mm to 8.1 mm after correction. The reversal error correction method proposed in this paper effectively reduces the reversal error caused by the energy fluctuation of laser echo pulse in the photon counting 3D imaging lidar.