Heavy metal stress will damage the normal growth and change the bio-parameters like chlorophyll, nitrogen and water content of rice. Simple, speedy, non-invasive test of heavy metal stress to crops means a lot to the agriculture and even the suspend of human being. Many traditional spectral index computed using hyperspectral data can inverse the above bio-parameters. While it is found that some indies do not work well when the heavy metal stress exists, however, some indies still has ability to estimate the above three bio-parameters. In this paper, 28 vegetation Indies were checked to make certain of their ability to reverse the bio-parameters of rice when there were heavy metal stress. A method to classify the stress level based on both the physical mechanism analysis and the statistic model are proposed. The 3-axes spectral indices spaces, which are constructed of 3 spectral indices sensitive to rice's chlorophyll concentration, nitrogen concentration and water concentration respectively, are used to visualize the linkage between heavy metal stress and spectrum of rice canopy.