With the advantage of high sensitivity and high repetition rate, spaceborne photon counting Lidar has shown great application in ocean areas. The photon counting detector can not only respond to the weak echo signal, but is also susceptible to solar radiation. Due to the great impact of background noise on the performance of Lidar systems, as well as the impact on the data volume, accurate estimation of noise level is crucial in the design of satellite Lidar systems. A noise model of oceanic spaceborne photon counting Lidar was proposed that considers the contribution of the atmosphere, water surface, and water column. By inputting the system parameters of the new generation photon counting Lidar ATLAS and the environmental parameters, the MAPEs (mean absolute percentage errors) between estimated noise and the ATLAS measured noise are within 15%, which confirms the effectiveness of the noise model.