In order to elucidate the effects of different water and nitrogen management modes on rice yield and soil carbon, nitrogen and phosphorus stoichiometry characteristics in black soil, an field experiment was conducted, in which, 3 irrigation modes (F, conventional flooding irrigation; S, shallow wet irrigation; C, controlled irrigation) and 4 nitrogen application gradients (N0, 0; N1, 85 kg/hm²; N2, 110 kg/hm²; N3, 135 kg/hm²) were set up, and then rice yields, the contents of soil carbon, nitrogen and phosphorus, stoichiometric ratios and stratification rates were determined under different treatments. The results showed that, compared with F and S, rice yield under C was significantly increased through the formation of sufficient large panicles to increase storage capacity and slightly increase seed setting rate (P<0.05). The contents of soil organic carbon (SOC), total nitrogen (STN), and total phosphorus (STP) decreased with the increase of soil depth. Nitrogen application treatments significantly increased SOC and STN contents but decreased STP content (P<0.05). Compared with S and C, SOC and STN contents were increased under F. Compared with F and S, STP content was increased under C. Soil C/N decreased but soil C/P and N/P increased with the increase of nitrogen application rate. Nitrogen application improved the average C/N stratification rates but reduced the C/P and N/P stratification rates of different soil layers, and compared with F, C improved the stratification rates of SOC and STP contents in different soil layers. In conclusion, C with appropriate nitrogen fertilizer can improve soil quality, and C with 110 kg/hm² nitrogen fertilizer is considered as the optimal water and nitrogen management method.