【Objective】The objective of this study was to investigate the effects of flooding stress and spraying exogenous cytokinin on root respiratory enzymes activities, endogenous hormone content and pod yield at different peanut growth stages, so as to provide a theory base for improving peanut resistance to flooding and using exogenous cytokinin hormone to regulate peanut growth. 【Method】Peanut (Shanhua108) was grown in the pot culture experiments with flooding treatment during 10 days at the seedling stage (V3), the flower needle stage (R3), the pod setting stage (R5), and the full fruit stage (R7),respectively. And the normal water management during the whole growth period (CK) was used as the control. Exogenous 6-benzyladenine (6-BA) (15 mg·L-1) were sprayed to the whole plants at a rate of 250 mL·m-2 after waterlogging. A total of 9 spraying combinations, namely, normal water management during the whole growth period (CK), flooding at the seedling stage (V3-W), spraying 6-BA after flooding at the seedling stage (V3-S), and flooding at the flower needle stage (R3-W), spraying 6-BA after flooding at the flower needle stage (R3-S), flooding at the pod setting stage (R5-W), spraying 6-BA after flooding at the pod setting stage(R5-S), flooding at full fruit stage (R7-W), spraying 6-BA after flooding at full fruit stage (R7-S). And then the anaerobic respiratory enzymes, aerobic respiratory enzymes activity, endogenous hormone contents, root dry weight (RDW), and root length density (RLD) were determined every 5 days after treatment. 【Result】The RDW and RLD in 20-60 cm soil layers were significantly decreased by waterlogging treatment. There was no root system in 20-40 cm soil layer under V3-W treatment after waterlogging. Compared with the R3-W treatment, the values of RDW and RLD of the 20-60 cm soil layer under the R3-S treatment was increased by 5.15% and 8.59% in the growing seasons of 2018 and 2019, respectively. Flooding stress increased the activities of Alcohol dehydrogenase (ADH), Lactate dehydrogenase (LDH), and decreased the activity of Malate dehydrogenase (MDH). For example, the activity of ADH and LDH was increased under V3-W treatment by 12.49 and 18.99 times, respectively. Whereas, the activity of MDH decreased by 65.15%. In addition, compared with CK treatment, ABA content in the two growing seasons was increased by 22.51%, 15.81%, 10.57% and 5.64% under V3-W, R3-W, R5-W and R7-W, respectively. However, spraying 6-BA significantly reduced the ABA content during R3 stage, which was 7.60% lower than that of R3-W treatment. On the contrary, endogenous ZR content was reduced by flooding stress at all the growth stages. Compared to CK treatment, ZR content under V3-W, R3-W, R5-W and R7-W treatment was decreased by 16.84%, 15.61%, 15.35%, and 8.51%, respectively. While application of exogenous 6-BA decreased the ABA content, but increased the ZR content. Flooding significantly reduced the number of fruit per plant and the yield per plant in the R5 period, which decreased by 38.39% and 30.43% in 2018, respectively, and decreased by 31.60% and 25.06% in 2019. The R3 period was sprayed with 6-BA in the growth season of 2018 and 2019, increased production by 5.38% and 6.91%, respectively. 【Conclusion】 Application of exogenous 6-BA after flooding increased peanut yield due to increasing root respiration performance and the leaf photosynthetic productivity resulting from reducing the root ABA content and increasing the ZR content to enhance root ADH and MDH activity, and to increase leaf chlorophyll content and photosynthetic rate.