Abstract:[Background] The antioxidant system plays an important role in plant tolerance to stress, and whether rhizobia affect the antioxidant system of legumes to improve plant tolerance to stress remains unclear. [Objective] Pongamia pinnata with strong stress tolerance was selected as the representative of legumes in this study, and the pot experiments of inoculating Rhizobium sp. PP3 to P. pinnata under nickel stress were performed. [Methods] The activities of four antioxidant enzymes and the content of four non-enzymatic antioxidants in the roots, stems and leaves of P. pinnata in different treatments were determined by the enzyme linked immunosorbent assay. [Results] The activities of antioxidant enzymes in P. pinnata followed the trend of superoxide dismutase (SOD)>peroxidase (POD)>catalase (CAT)>glutathione reductase (GR), and the content non-enzymatic antioxidants was in the order of glutathione (GSH)>flavonoid (FLA)>oligomeric proantho cyanidins (OPC)>ascorbic acid (AsA). In the case of no nitrogen supply and 40 mg/L Ni2+ stress, Rhizobium sp. PP3 increased the POD activity in the stems by 61.8%, and the SOD, GR, and CAT activities in the leaves by 5.7%, 23.6%, and 36.1%, respectively. Under the stress of nitrogen and 40 mg/L Ni2+, Rhizobium sp. PP3 increased the content of GSH, FLA, and OPC in the roots by 55.9%, 61.6%, and 38.6%, respectively, and the GSH content in the leaves by 14.8% under the stress of 40 mg/L Ni2+. [Conclusion] Rhizobia had significant effects on the four antioxidant enzymes and non-enzymatic antioxidants in P. pinnata, while the effects on antioxidant enzymes and antioxidants varied in different tissues. The results indicate that rhizobia regulate the antioxidant system of P. pinnata in response to nickel stress, and they play a role in strengthening the stress tolerance of P. pinnata in the nickel-contaminated soil.