Appropriate irrigation methods and N management can effectively increase the yield and N efficiency of rice (Oryza sativa L.). A soil‐grown experiment was conducted in 2018 and 2019 using Liangeng 7 with different N forms (NH3–N, NH4+ and NO3− mixed 50:50 [50:50], and NO3–N), as well as three irrigation regimes (submerged irrigation [0 kPa], alternate wetting and moderate drying [−20 kPa], and alternate wetting and severe drying [−40 kPa]). Results showed that yield and N agronomic efficiency were maximized at the alternative wetting and moderate dying treatment with NH4NO3 mixed among all treatments. Nitrogen forms in different irrigation regimes had different effects on root characteristic and leaf photosynthesis rate. In submerged irrigation, NH3–N treatment improved root morphology, increased the activities of NH3 assimilation enzymes in roots, and promoted root oxidation and leaf photosynthesis rate at different growth stages compared with other N forms. By contrast, moderate drying interacted with 50:50 and significantly enhanced root length, average root diameter, root volume, root tips, and root oxidation activity and promoted C and N metabolism in root and photosynthesis rate of leaves compared with other N forms under alternate wetting and drying irrigation. Multiple regression analysis showed that root length, the glutamate synthase (GOGAT) activity of roots, and the photosynthetic rate of leaves closely related with high rice yield and efficient N utilization. All these results suggested that improved root morphology and physiology activity, enhanced C and N metabolism, and increased leaf photosynthesis rate through the appropriate regulation of irrigation‐regime interaction with N forms can help to increase the grain yield and N agronomic efficiency of rice.