In order to explore the difference in the resistance physiology and yield, and the mitigation effect of uniconazole（S3307） pretreatment under waterlogging stress, the pot experiment in this research was conducted, and the crop cultivar including Longhongdou4（LHD 4） and Tianjinhong（TJH）. Waterlogging treatment and foliar spraying of S3307 were carried out at the seedling stage of adzuki bean. The lasting time of waterlogging stress in the experiment was 5 days. And samples were taken every day to determine and analyze the related physiological indexes and yield factors. The results showed that flooding stress at seedling stage significantly increased the contents of H₂O₂ and MDA, proline and soluble protein, and the activities of SOD, POD and CAT in the stem of adzuki bean. Flooding treatment for 5 days significantly decreased the yield of LHD 4 by 8.40% and TJH by 9.88%. S3307 can resist flooding stress, effectively increase the contents of proline and soluble protein in young stems of adzuki bean, significantly reduce the contents of H₂O₂ and MDA, and significantly increase the activities of SOD and POD. Spraying S3307 significantly increased the yield of LHD 4 and TJH by 2.75% and 5.29%, respectively.