Objective Previous studies have shown that root-zone application fertilization of controlled-release urea (ZRFCRU) can increase the yield and nitrogen use efficiency of ratoon rice; however, the underlying physiological mechanisms remain unclear. This study investigated the effects of alternate wetting and drying irrigation combined with one-time ZRFCRU on leaf physiological characteristics and yield of ratoon rice, aiming to provide a theoretical basis for simplified fertilization and integrated water-nitrogen management in ratoon rice production.

Methods A pot experiment was conducted using a two-factor randomized complete block design with irrigation regimes and nitrogen application methods. The irrigation regimes included conventional continuous flooding irrigation (CI) and alternate wetting and drying irrigation (AWD). Five nitrogen application treatments were established: no nitrogen (CK), farmers’ conventional fertilization practice (FFP), one-time shallow ZRFCRU (CUR1), one-time deep ZRFCRU (CUR2), and one-time layered ZRFCRU (CUR3). Yield and nitrogen accumulation were measured in both the main and ratoon seasons. Physiological characteristics including plant height, leaf area index (LAI), leaf SPAD value, photosynthetic rate, and leaf nitrogen metabolism enzyme activities were analyzed. Additionally, the number of effective panicles at each node and their contribution to ratoon season yield were examined. A random forest model was used to identify the key physiological indicators and limiting factors affecting ratoon rice yield.

Results Compared with the FFP under both irrigation regimes, the AWD+CUR3 significantly increased nitrogen accumulation and leaf nitrogen metabolism enzyme activities in both seasons. Specifically, the main-season yield was significantly increased by 33.9% and 23.4%, respectively, and the ratoon-season yield was significantly increased by 22.4% compared with AWD+FFP. Yield component analysis showed that the CUR3 significantly increased the number of effective panicles and grains per panicle in both seasons compared with FFP. Yield was significantly positively correlated with leaf physiological characteristics (e.g., nitrogen metabolism enzyme activities). Grains per panicle, NR activity, effective panicle number, and LAI were the main limiting factors for yield increase in the main season, while effective panicle number was the main limiting factor for yield increase in the ratoon season. Compared with the FFP under both irrigation regimes, the AWD+CUR3 in the ratoon season significantly increased yield primarily by increasing the number of effective panicles at the second node from the top (by 16.3% and 12.9%, respectively). The second and third nodes from the top were the main contributing nodes for ratoon season yield, together accounting for more than 72.09% of the total yield.

Conclusions Alternate wetting and drying irrigation combined with one-time root-zone layered application of controlled-release urea (AWD+CUR3) significantly increased nitrogen accumulation, leaf relative chlorophyll content, nitrogen metabolism enzyme activities (NR, GS, GOGAT), and photosynthetic capacity in both the main and ratoon seasons of ratoon rice. It also significantly increased the number of effective panicles and yield at the main contributing nodes (the second and third nodes from the top) in the ratoon season, thereby achieving higher yields in both seasons. The results provide a theoretical foundation for the green production of ratoon rice.