The objective of the study was to determine the physiological mechanisms of plants in response to brassinolide (BR) alleviating cold water stress on rice. In this study, physiological responses of rice to exogenous BR and cold water submergence were investigated using the chilling-tolerant cultivar Kongyu 131 (KY131) and the chilling-sensitive cultivar Kenjiandao 6 (KJD6). A total of 2 mg L–1 BR increased activities of superoxide dismutase (SOD) and peroxidase (POD) and the contents of soluble sugar, soluble protein, and chlorophyll, but decreased the malondialdehyde (MDA) content in KY131 and KJD6 under cold water stress. The observed decreases in SOD and POD activities and MDA content recovered quickly after plants were reted to irrigation with water at temperatures of about 23.0℃ in 2014. Additionally, the contents of nitrogen (N), phosphorous (P), and potassium (K) were increased by BR treatment under cold water stress. Exposure to BR also raised the percentage of high effective leaf area and leaf area index at the heading stage. Furthermore, it promoted soluble sugar synthesis, increased the rate of dry matter accumulation, and enhanced the export and translocation rates of the stem-sheath. The yield in KJD6 was significantly (P≤0.01 and P≤0.05) higher than that of the control in 2013 and 2014, respectively. The effect of BR treatment on rice leaf SOD and POD activities, MDA, chlorophyll, P, and stem-sheath K contents were more significant in KJD6 than in KY131. In conclusion, exogenous BR effectively reduced the physiological and metabolic damage in rice due to cold stress at the booting stage, promoted functional recovery in plants that received irrigation with water at a normal temperature following cold stress, and mitigated the effects of cold water stress on yield.The two varieties exhibited differential responses to BR; the weaker cold-resistant variety was more sensitive to BR and displayed stronger responses to exogenous BR.