Based on the data of underwater light field measured in Taihu lake and Tianmuhu lake, on the supposition that there is source-free and no inelastic-scattering water, the inherent optical property (absorption coefficient) of medium in shallow lakes was successfully inversed by using the profile of upward and downward irradiance, diffuse reflectivity and diffuse decay coefficient.The error aroused from surface wave and ship shadow was reduced by the inversion method. The inversion results agree well with that by using the quantitative filter technique (QFT). The method is helpful to research on photosynthesis available radiation distribution among different media and aquatic ecology responding to underwater light field, to mechanism of cyanobacteria bloom and to remote sensing precision for case 2 water improved.