Rice is challenged by inefficient nitrogen (N) fertilizer and water inputs. However, pH-responsive N fertilizers (pH-RNFs) could improve rice yield and N use-efficiency under water-saving irrigation. Thus, a pot experiment was conducted without N fertilizer (0 mg N/kg, ZNF), with 175 mg/kg mineral N fertilizer (MNF), and with 175 mg/kg pH-responsive N fertilizer (pH-RNF) by using three water regimes: alternate wetting/critical drying (AWCD, 70–60% saturation, 5 cm flooded), alternate wetting/severe drying (AWSD, 80–70% saturation, 5 cm flooded), and alternate wetting/minor drying (AWMD, 100–90% saturation, 5 cm flooded). Under the same alternate wetting/drying regime, the growth traits, yield, and N utilization of rice were found to be higher in pH-RNF than in MNF. The growth attributes and yield and the N efficient use of rice were greater in the AWMD regime than in the AWCD regime under the same N fertilization. The surface area, diameter, length density, oxidation ability, reductase activity, and peroxidase activity of roots were greater in AWMD × pH-RNF than in AWCD × ZNF, because the former treatment increased the total N contents in the rhizosphere, whereas the latter reduced them. In the photosynthesis process, leaf nitrate reductase (41.7 µg/[g.h]) and leaf glutamine synthetase (1158.1 µmol/[g.h]) were larger in AWMD × pH-RNF than in AWCD × ZNF at 22.7 µg/(g.h) and 501.2 µmol/(g.h), respectively, resulting in the amelioration of oxidative leaf cell damage, as revealed by reduced radical oxidative sequence release and lower malonaldehyde level (7.2 µmol/g). Meanwhile, the optimum N nutrition enhanced the leaf mesophyll structure, cell cycle progression, and the development traits of the stem and panicle under the combination AWMD × pH-RNF. Panicle glutamine synthetase (24.35 µmol/[g.h]) and catalase activity (13.86 µg/min) were larger in AWMD × pH-RNF than in AWCD × ZNF at 14.77 µmol/[g.h] and 7.59 µg/min, respectively. The combination AWMD × pH-RNF resulted in the highest N crop removal efficiency (CREN, 49.5%), N agronomic use efficiency (AUEN, 7.97 g/g), N partial factor productivity (PFPN, 18.66 g/g), and N harvest index (HIN, 67.83%). However, the minimum values of CREN (10.3%), AUEN (1.49 g/g), PFPN (7.59 g/g), and HIN (43.48%) were observed in AWCD × MNF. This study suggests that AWMD × pH-RNF could promote root and shoot morpho-physio-biochemical traits, guaranteeing optimal overall plant growth with high yield and adequate N acquisition, and efficient N utilization for sustainable rice production.
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