In the underwater application of lidar, the underwater transmission of laser light is complicated and variable due to the absorption and scattering of light by water, especially the noise caused by backscattering will reduce the contrast of the target, and the target echo even will be drown, resulting in big challenges of water downward laser echo detection. The subcarrier modulation technology can effectively improve the underwater detection performance of the lidar system and increase the signal-to-noise ratio of the target echo signal. Based on the Monte Carlo method, an improved underwater transmission model of a subcarrier-modulated pulsed lidar was proposed. The effects of seawater attenuation coefficient and passband on system performance were studied. Simulation results show that compared with traditional lidar, the environmental parameters of the water body and the selection of the passband during filtering have a greater impact on the underwater detection performance of the system; the subcarrier modulation technology can improve the target signal-to-noise ratio and measurement accuracy, it effectively improve the system performance.