The roles of different concentrations of arsenite (As(III)) and cadmium (Cd) (0, 25 and 50 μM) in the absence and presence (1.7 mM) of phosphate (P) in tolerance and antioxidant genes expression in Oryza sativa L. were investigated. The growth parameters, metal accumulation, lipid peroxidation and soluble protein and 17 genes involved in metal accumulation and oxidative stress were measured. In our results, Lsi6 (OsNIP2;2) could play an important role in As(III) accumulation of shoots and roots in P supply (+P) and deficiency (-P) plant, while OsNRAMP5 was attributed to the part of As(III) uptake though roots under -P condition. Both of Lsi6 and OsNRAMP5 could involve Cd uptake of roots in +P plant. OsNRAMP1 was a main transporter for As(III) and Cd uptake in roots of -P plant. However, +P increased the soluble protein contents and reduced the lipid peroxidation under As(III) or Cd exposures. In As(III) exposed rice seedlings, SOD, CAT, POD, GPX, AsA-GSH cycle and GSH metabolism process were provoked to eliminate ROS induced by As(III), especially under -P condition. In Cd exposed rice seedlings, AsA-GSH cycle and GSH metabolism process played a main role in the detoxification process of plant cells, and +P could promote enzyme system activity. Furthermore, +P improve the tolerance ability of plants to tolerant 50 μM As(III) and Cd exposures compared to P deficiency.