A Monte Carlo radiative transfer model with polarization was developed to simulate and analyze the vertical profile of received polarization signal of a ship-borne lidar. The measurement errors resulted from different seawater optical parameters and various lidar measurement modes were analyzed as well. A Gaussian distribution function was used to describe the chlorophyll-a vertical profile. The scattering layers were set at 10-30 m with the low, medium and high values of chlorophyll-a concentration ([chl-a]), respectively, and the corresponding maximum value of [chl-a] was 0.1 mg/m³, 1 mg/m³ and 10 mg/m³, respectively. The polarization return signals of the ship-borne oceanographic lidar were simulated with a laser transmission wavelength of 532 nm and field of views (FOVs) of 10-1000 mrad, and the main factors affecting the polarization measurement error were analyzed. The results suggest that the single scattering ratio of lidar return signal decreases with the enhancements of detection depth, [chl-a] and FOV due to the multiple scattering process of laser transferring in seawater. This leads to an increase in the error of the depolarization ratio directly measured by lidar. Let’s take the FOV of 100 mrad as an example. In the case of the scattering layer with a medium [chl-a], the relative errors of the depolarization ratio above (0-10 m), in (10-30 m) and under (30-40 m) the scattering layer were 16%, 125% and 281%, respectively. In the scattering layer, the relative errors of the depolarization ratio were 54%, 125% and 731% for the low, medium and high values of [chl-a], respectively. When the FOV increases from 10 mrad to 1000 mrad, the relative error of the depolarization ratio increases from 6%-28% above the scattering layer, 17%-452% in the scattering layer and 10%-734% under the scattering layer, respectively, for the case of the scattering layer with a medium [chl-a]. Therefore, when using the polarization oceanographic lidar to detect the seawater depolarization ratio, the traditional algorithm for depolarization ratio will introduce a large error due to the multiple scattering process, and a correction is required to improve the detection accuracy of lidar measurement.