Atmospheric correction is a bottleneck in quantitative application of Chinese satellites HJ-1 data to remote sensing of water color. According to the characteristics of CCD sensors, the present paper made use of air-water coupled radiative transfer model to work out the look-up table (LUT) of atmospheric corrected parameters, and thereafter developed pixel-by-pixel atmospheric correction method over waters accomplishing the water-leaving remote sensing reflectance with accessorial meteorological input. The paper validates the HJ-1 CCD retrievals with MODIS and in-situ results. It was found that the accuracy in blue and green bands is good. However, the accuracy in red or NIR bands is much worse than blue or green ones. It was also demonstrated that the aerosol model is a sensitive factor to the atmospheric correction accuracy.