Nitrogen (N) application rates and irrigation regimes are key factors determining rice yield and N use efficiency. To evaluate the effects of different irrigation regimes and N application rates on rice yield and N uptake, a four-year field experiment was conducted from 2021 to 2024 at the Qing’an National Irrigation Experimental Station in Heilongjiang Province. The experiment included two irrigation regimes (C: Controlled irrigation and F: Flooded irrigation) combined with four N application rates (N0: 0 kg N·ha⁻¹, N1: 82.5 kg N·ha⁻¹, N2: 110 kg N·ha⁻¹, and N3: 137.5 kg N·ha⁻¹). The results showed that, considering the same N application rate, C promoted dry matter accumulation by 3% to 9% and total N accumulation by 4.1% to 25.5% in the aboveground parts of rice compared to F. Under the same irrigation regime, total N accumulation in the aboveground parts of rice increased with N application rate and then plateaued. Regarding the distribution of N among organs, the proportion of panicle N relative to total N in the aboveground parts of rice followed an initial increase and subsequent decline as N input increased, resulting in the nitrogen harvest index (NHI) reaching its maximum under the moderate N treatment (N2). Overall, controlled irrigation significantly improved the NHI and AE, whereas the moderate N treatment (N2) further increased the NHI and promoted greater N allocation to panicles. Therefore, combining C with a moderate N application rate can enhance N use efficiency and markedly improve the internal N partitioning pattern.