A field plot comparison experiment was conducted to study the strong stem effect and physiological characteristics of rice plant under rice-duck farming. The results showed that under rice-duck farming, the morphology of rice plant changed obviously, and the carbohydrate content and C/N ratio of the plant as well as the dry matter output from rice stem increased significantly, due to the activities of duck in paddy field. In the meantime, the length of basal internodes decreased by 2. 88%, while the stem diameter, stem mechanical strength, and stem lodging resistant index increased by 64.90%, 11.78%, and 10.95%, respectively. Rice-duck farming increased the root mass and root vitality in deeper soil layers, and decreased the proportion of black roots by 16.63%. It was indicated that rice-duck farming benefited the formation of strong rice stem and increased the stress resistance of rice plant, which would be favorable to the stable and high-yielding of rice.