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In order to clarify the response mechanism of carbon, nitrogen and phosphorus absorption, accumulation and allocation in black soil rice to water-nitrogen coupling mode and analyze the nitrogen and phosphorus nutrient restriction, three irrigation models, conventional flooded irrigation (F), shallow wet irrigation (S) and controlled irrigation (C), and four nitrogen application levels 0kg/hm2, 85kg/hm2, 110kg/hm2 and 135kg/hm2(N0, N1, N2, N3), were set up in the experiment, which were a total of 12 treatments. To study the effects of different water-nitrogen coupling modes on carbon, nitrogen and phosphorus contents, accumulation, allocation ratio, stoichiometric ratio and nitrogen, phosphorus nutrient restriction of rice plants during each growth periods. The results showed that under different water-nitrogen coupling treatments, the contents of carbon, nitrogen and phosphorus in stem sheaths were 35.87%~39.43%, 0.44%~2.19% and 0.14%~0.32%, respectively, and the contents of carbon, nitrogen and phosphorus in leaves were 36.34%~40.83%, 0.76%~3.70% and 0.14%~0.36%, respectively and the contents of carbon, nitrogen and phosphorus in panicle were 37.05%~41.72%, 0.82%~1.63% and 0.24%~0.39%, respectively. Controlled irrigation could increase the carbon and nitrogen accumulation from jointing booting stage to mature stage, and the phosphorus accumulation during the growth period of conventional flooded irrigation was always higher than that of shallow wet irrigation and controlled irrigation. Under three irrigation modes, compared with N0, N1, N2 and N3 treatments increased carbon accumulation by 31.46%, 52.55% and 57.37%, nitrogen accumulation was increased by 52.98%, 117.63% and 144.88%, and phosphorus accumulation was increased by 50.28%, 79.85% and 93.89%, respectively, at maturity stage. The proportion of carbon, nitrogen and phosphorus in stem sheaths was increased first and then decreased, the proportion of carbon, nitrogen and phosphorus in leaves was decreased continuously, and the proportion of carbon, nitrogen and phosphorus in panicle was increased continuously. Compared with conventional flooded irrigation and shallow wet irrigation, the controlled irrigation mode had less effect on the carbon content of rice plants, but it can increase the nitrogen content in the middle and late stages of rice plant growth, and reduce the plant phosphorus content, thereby reducing rice plant C/N and increasing rice plant C/P and N/P. Nitrogen application significantly increased the nitrogen content of rice plants, slightly increased the phosphorus content of rice plants, and had relatively little effect on the carbon content of rice plants, and then decreased the C/N and C/P of rice plants, and increased the N/P of rice plants. Under conventional flooded irrigation and shallow wet irrigation, the nutrition of shoot plants of rice transited from phosphorus restriction to nitrogen and phosphorus co-restriction and then to nitrogen restriction, while under controlled irrigation, shoot plants of rice only transited from phosphorus restriction to nitrogen and phosphorus co-restriction. In general, controlled irrigation can promote nitrogen absorption and increase rice yield, and it can be considered comprehensively that CN2 can be the best water-nitrogen coupling mode.