The rice waterlogging stress test was conducted at the experimental base of the College of Agriculture, Yangtze University, using Yangxian You 418 as the test subject, in order to investigate the impact of waterlogging on rice growth during the period from July to August each year. Six waterlogging stress tests with different waterlogging depth (1/4 plant height (1/4PH), 2/4 PH, and 3/4 PH) and duration (5 d and 7 d) were set up at the jointing–booting stage of rice (T1: 1/4 PH, 7 d; T2: 2/4 PH, 7 d; T3: 3/4 PH, 7 d; T4: 1/4 PH, 5 d; T5: 2/4 PH, 5 d; T6: 3/4 PH, 5 d;) with shallow water irrigation (CK) as control. The plant height, population leaf area, above-ground dry matter, and the yield of rice were measured. The correlation between the waterlogging depth and rice yield reduction was analyzed, and the flood disaster threshold index of rice was established. The results showed that at the end of stress, the plant height of all waterlogged treatments exceeded CK, and the plant height of T3 and T6 treatments significantly increased by 31.90% and 15.93%, respectively. The leaf area of rice treated with T1, T3, T4, and T5 was higher than CK (p < 0.05), and the above-ground dry matter of rice treated with T2, T3, T4, T5, and T6 was higher than CK (p < 0.05). When normal irrigation was restored to the maturity stage, the plant height of all rice treated with waterlogging was still higher than CK (p < 0.05). However, as the degree of waterlogging increased, rice yield decreased significantly, with a notable reduction of 31.68% observed in the T3 treatment compared to CK. Assuming a drainage index based on a 20% decrease in rice yield, it is imperative that the ratio of flooded depth to plant height remains below 37% when waterlogging persists for 7 days in rice cultivation. These research findings offer crucial scientific insights for implementing effective drainage management measures during flood disasters in rice paddies.