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The present study investigated the effects of different integrated cultivation treatments on the yield, nitrogen agronomic efficiency (AE_N), and growth performance of a ratoon rice system. A two-year field experiment was carried out during 2021–2022 using a randomized block design. Cultivation treatments included the farmers’ practice model (control, CK), high-yield and high-efficiency model (T1), enhanced-high-yield and high-efficiency model (T2), and the no-N model (N0). The grain yield, yield components, root traits, and stubble characteristics were determined. The results showed that T2 treatment significantly increased the grain yield and AE_N by 53% and 236%, respectively, compared with CK. Similarly, the stubble weight, non-structure carbohydrate contents, and the root attributes were significantly improved under T2 treatment. The correlation analysis suggested that ratoon rice yield and AE_N was significantly and positively correlated with root weight (<i>p</i> < 0.01) and the stubble parameters including stubble weight (<i>p</i> < 0.01), starch content (<i>p</i> < 0.01), and soluble sugar content (<i>p</i> < 0.01). Additionally, a significant and positive correlation between root weight and stubble weight (<i>p</i> < 0.05) was determined in our study. Consequently, our work highlights the benefits of integrating planting density, nitrogen/water management, and other practices to achieve high AE_N and grain yield of the ratoon rice by improving root trait and stubble characteristics of the main rice.