Based on the models of hydrodynamics and radiation transfer, the remote sensing reflectance (Rrs) affected by different water constituents′ vertical distribution under the condition of different wind speeds is simulated. The calibration effect of two different water optical homogeneous functions (Zaneveld and Gordon weight function) in the stratified water mass is compared and analyzed. The results indicate that the Rrs in the range of 500~650 nm is significantly affected by the vertical distribution of suspended particle. With the increasing of suspended particle concentration (5~70 mg/L) at reference depth, the influence of suspended particle matter vertical distribution to the Rrs becomes smaller and smaller (the variation coefficient induced by suspended particle decreases from 27.46% to 3.38%). And the biggest influencing wavelength position on Rrs moves to the long wavelength (585~685 nm). With the increasing of wind speed, the influence of phytoplankton vertical distribution on Rrs in the range of 400~725 nm increases firstly and then decreases. The influence of phytoplankton vertical distribution on Rrs in the range of 400~450 nm is the smallest. The variation coefficient induced by phytoplankton vertical distribution is only 1%. The influence of phytoplankton vertical distribution on Rrs in the range of 500~600nm is the biggest. The variation coefficient induced by phytoplankton vertical distribution can reach 27.18%. The effect of optical homogeneous calibration by the Zaneveld weight function is similar with Gordon weight function when the stratification of water mass is insignificant. However, the effect of optical homogeneous calibration by the Zaneveld weight function is better than Gordon weight function when the stratification of water mass is significant.