Organic fertilizers can substitute for part of the basal fertilizers under water-saving irrigation. This study aims to explore the effects of the combined organic and inorganic fertilizers on the uptake and utilization of topdressing nitrogen at the late growth stage of rice in a black soil paddy field. Field- and micro-plot experiments were employed under controlled irrigation. The 15N tracer technique was also utilized to label the applied topdressing fertilizers (tillering and panicle fertilizers). Flooding irrigation with conventional nitrogen application (CK) served as the control. Five gradients of organic and nitrogen substitute basal fertilizers were set under water-saving irrigation: conventional application of chemical nitrogen fertilizer (CF0), organic fertilizer instead of 20% basal fertilizer (CF1), organic fertilizer instead of 40% basal fertilizer (CF2), organic fertilizer instead of 60% basal fertilizer (CF3), and 80% basal fertilizer (CF4). A systematic investigation was made on the absorption, utilization, and translocation of topdressing nitrogen in the paddy field. Different proportions of organic fertilizer were selected to replace basal fertilizers in the water-saving irrigation. The distribution of topdressing nitrogen was obtained in various plant organs at the rice maturity stage. Experimental results demonstrate that the CF3 significantly improved several key parameters of the growth yield of rice. Specifically, the substitution markedly enhanced the above-ground dry matter accumulation, total nitrogen uptake, and grain yield at the physiological maturity stage of the crop. Furthermore, the amount of topdressing nitrogen absorbed by rice plants varied between 26.20 and 33.89 kg/hm² among treatments with different substitution ratios of the organic fertilizer under controlled irrigation. There was a substantial increase, compared with the CK. Notably, the CF3 treatment exhibited a 29.36% greater than the CF0. The efficiency of topdressing nitrogen utilization ranged from 43.74% to 61.62% among the various organic substitutions. Importantly, controlled irrigation consistently resulted in higher nitrogen use efficiency under identical nitrogen application levels, compared with conventional flooding irrigation. The controlled irrigation with partial organic fertilizer substitution was realized to optimize nitrogen resources for rice production. The contribution rates of topdressing nitrogen to total nitrogen accumulation ranged from 14.21% to 16.12% under controlled irrigation with the organic manure substitution. However, no significant difference was detected between the two irrigation modes under conventional nitrogen application. Substituting 60% of basal fertilizers with organic fertilizer significantly enhanced the translocation contribution of topdressing nitrogen to grain nitrogen accumulation under controlled irrigation. Nitrogen fertilizer use efficiency was improved to modify the distribution pattern of topdressing nitrogen in the different rice organs. Correlation analysis revealed that there were significant positive relationships (P < 0.05) between topdressing nitrogen utilization efficiency and the contribution ratios to grain translocation and accumulation percentage in organs under the total nitrogen. In summary, the CF3 can be expected to offer high yields and efficient utilization of topdressing fertilizers. The optimal ratio was also obtained for the organic fertilizer substitution. The finding can provide a theoretical basis and technical reference to further improve the utilization rate of fertilizer nitrogen in paddy fields in the black soil region of cold areas.