Abstract: By taking the rice varieties of Nipponbare and Lemont as the materials, the effects of Cd stress on the content of pigment, the subcellular distribution of Cd and the content of free amino acid in different rice varieties were explored by being treated with adding different concentrations of Cd in the hydroponic nutrient solution. The results showed that with the increase of Cd concentration, the two kinds of rice showed a decreasing trend of the contents of chlorophyll and carotenoid, while the content of Cd in cell wall, cytoplasm and organelle increased significantly. The Cd content in cell wall of the rice varieties of Nipponbare and Lemont under different treatments accounted for 86.24%-88.59% and 88.66%-94.17% of the total contents of Cd in cells, respectively, indicating that the cell wall was the main part of Cd accumulation in rice. When treated with Cd of 50 μmol·L^-1 and Cd of 100 μmol·L^-1, the contents of proline, cysteine and glutamic acid in the two rice varieties of Nipponbare and Lemont increased significantly with the increase of Cd concentration. Under the treatment of 50 μmol·L^-1 Cd, the contents of alanine, phenylalanine, methionine and glycine in the two rice varieties could be increased significantly. However, under the treatment of 100 μmol·L^-1 Cd, However, the contents of phenylalanine and methionine in Nipponbare rice and alanine, methionine and glycine in Lemont rice were not significantly increased. In summary, under the stress of Cd, the two rice varieties enhanced the resistance of Cd by adjusting the subcellular distribution of Cd and accumulating the content of free amino acids, and showed the genotypic differences between Nipponbare and Lemont varieties.