To explore the traits and mechanical characteristics of lodging-resistant stems of high-quality late-season rice under water-nitrogen interaction conditions, this study used the high-quality late-season rice variety Nongxiang 42 as the test material and designed a split-plot experiment. Water management served as the main-plot factor, with two treatments: alternate wetting and drying (W1) and continuous flooding(W2). Nitrogen fertilizer management acted as the sub-plot factor, with three nitrogen application levels set at 120 kg/hm² (N1), 180 kg/hm² (N2), and 240 kg/hm² (N3). The results indicated that nitrogen fertilizer management significantly influenced rice plant height, center-of-gravity height, center-of-gravity ratio, internode wall thickness, bending moment, and lodging index. Specifically, compared with the N1 treatment, the center-of-gravity height under the N2 and N3 treatments significantly increased by 11.08% and 15.32%, respectively, while the center-of-gravity ratio significantly increased by 9.36% and 12.93%, respectively. The internode wall thickness of the 3rd internodes under the N3 treatment significantly increased by 16.85%, while that of 4th internode significantly decreased by 12.00%. For the internode wall thickness of the 4th and 5th internodes under the N2 treatment significantly decreased by 24.67% and 8.70%, respectively. While the water-nitrogen interaction had a particularly notable impact on internode wall thickness, bending resistance, and lodging index. Under the same water management level, bending resistance showed a trend of first decreasing and then increasing with the increase in nitrogen application levels. Compared with the N1 treatment, the lodging indices of the 1st to 3rd internodes under the N2 treatment increased by 27.06%, 37.84%, and 25.51%, respectively. The lodging indices of the 4th and 5th internodes under the N2 and N3 treatments significantly increased by 74.38%, 65.01% and 60.37%, 64.19%, respectively. Correlation analysis revealed that the bending resistance of the 2nd to 4th internodes was significantly positively correlated with internode wall thickness, internode fullness, and bending modulus, and significantly negatively correlated with the maximum stress on the cross-section. The lodging indices of the 2nd to 4th internodes were significantly positively correlated with the center-of-gravity height and the maximum stress on the cross-section, and significantly negatively correlated with internode wall thickness and internode fullness. In conclusion, under a certain nitrogen fertilizer level (<180 kg/hm²), the use of alternate wetting and drying irrigation can effectively enhance the lodging resistance of the high-quality late-season rice variety Nongxiang 42 by improving its center-of-gravity height, center-of-gravity ratio, and internode wall thickness.