In this study, we took the high-quality late indica rice ‘Taiyou 553’ and ‘Yuzhenxiang’ as the test materials, and sprayed rice seedlings with paclobutrazol(15% paclobutrazol 1 500 g with 750 kg water) at the one-leaf-one-center stage and the two-leaf-one-center stage, and sprayed water as CK. At the maturity stage, we measured the agronomic traits and yield of rice, the physical traits of the stalks, the mechanics and lodging resistance traits, and analyzed the correlation between the lodging resistance traits of the plants and the main stem traits. The results showed that the spraying of paclobutrazol significantly increased the yield of ‘Taiyou 553’ in both periods, while it did not significantly increase the yield of ‘Yuzhenxiang’, in which the yields of ‘Taiyou 553’ in creased by 20.63% and 15.29% under the treatments of one-leaf-one-center stage and two-leaf-one-center stage, respectively, compared with the control treatment. Overall, the spraying had the tendency to reduce the plant height, shorten the internode length, increase the internode thickness and stem node wall thickness of the two rice varieties at the maturity stage, which in turn increased the internode fullness and fracture bending moment, and improved the lodging resistance. In addition, the spraying at the two-leaf-one-center stage improved the lodging resistance of ‘Yuzhenxiang’ more than that at the one-leaf-one-center stage, in which the lodging resistance index of ‘Yuzhenxiang’ under two-leaf-one-center treatment increased significantly by 36.46% compared with control, while the difference between the one-leaf-one-center stage treatment and the control treatment was not significant. The effect of paclobutrazol on the lodging resistance parameter of ‘Yuzhenxiang’ was higher than that of ‘Taiyou 553’. Reasonable spraying of paclobutrazol at the seedling stage could improve the yield and lodging resistance of rice at the maturity stage, with its long-lasting effect depending on the rice varieties.