Due to the complex optical properties of case II water, the application and inversion accuracy of water color remote sensing data can be reduced in the study of ocean water color remote sensing. The effect of relative spectral response and bandwidth of MODIS and TM channels on the water-leaving reflectance of optically complex case II water is analyzed. The analysis result shows that the effect of the relative spectral response and bandwidth of MODIS channels on water-leaving reflectance is much less than that of the corresponding TM channels. In addition, the quantitative analysis result shows that the relative spectral response and the bandwith have their different effect on the water-leaving reflectance of different channels and water types. According to three typical types of water at the mouth of Yangtze River, the water-leaving reflectance of the TM channels is used to simulate the reflectance of the entire channels. Thus, the spectral properties of case II water are characterized more obviously and the effect of the spectral response function and bandwidth is removed.