Abstract: In order to accurately reflect the optical signals received by the lidar, it is necessary to correct and calibrate the afterpulse characteristics of the photomultiplier tube. The probability distribution function of the afterpulse was used to analyse and verify the sounding data of the airborne marine lidar with wavelength of 486nm and 532nm, respectively, and the corrected results were compared with the data obtained by Monte Carlo simulation. The results show that the correlation between the calibration data and the Monte Carlo simulation data is as high as 0.9689(486nm) and 0.8648(532nm), respectively. About 98m(486nm) and 33m(532nm) false signals are eliminated based on the corrected data compared with the data before, and the accuracy of measurement of the airborne marine lidar is improved effectively. This research is helpful for the measurement of ocean depth and the study of submarine geomorphy.