Abstract: To date, ICESat-2/ATLAS has delivered numerous earth observation data products. Nevertheless, in practical aquatic environments, factors such as refraction effects at the air-water interface, water column inhomogeneity, and sea surface wave undulations lead to insufficient applicability of existing inversion algorithms for aquatic optical parameters, resulting in uncertain deviations between estimated values and true values. Additionally, due to the inherent afterpulse effect of photon-counting detectors, a small-amplitude pulse echo emerges subsequent to the main signal pulse, causing a systematic overestimation of measured signals. Therefore, this study proposes an inversion method for aquatic optical parameters using ICESat-2 lidar data, encompassing steps such as signal photon classification, error correction, aquatic pseudo-waveform generation, afterpulse removal, and aquatic parameter estimation. Large-scale comparative validation is conducted against MODIS optical parameters in the Gulf of Alaska (United States) and the East China Sea (China). Results demonstrate that the average errors of the diffuse attenuation coefficient (K_d) retrieved by ICESat-2 compared with MODIS products in the two regions are 17% and 18% respectively, while the corresponding average errors of the backscattering coefficient (b_b) are 24% and 41% respectively. This confirms the effectiveness of spaceborne photon-counting lidar in retrieving marine bio-optical parameters, which can serve as a reference for inversion algorithm development of future domestic spaceborne marine photon-counting lidar systems.