Two water management modes, namely, “alternating dry and wet” (RC) and “long-term deep water irrigation” (RS), were established in 2020 and 2021 to explore the effects of different water management modes on rice nitrogen use efficiency, rice quality and yield, crayfish yield and size distribution under rice shrimp co cropping mode. The results showed that compared with RC treatment, RS treatment had a trend to reduce rice nitrogen use efficiency and rice quality. In 2021, the nitrogen agronomic efficiency and amylose content of RS treatment were significantly lower than those of RC treatment, the protein content was significantly higher than that of RC treatment, and the comprehensive score of taste value was slightly lower than that of RC treatment (p>0.05). In the experiments in 2020 and 2021, the actual grain yield of RS treatment exceeded the stable yield target of 7.5 t/hm², and the difference with RC treatment is not significant. In addition, RS treatment could effectively increase the total yield and the yield which individual weight over 35 g（112.51%-115.56%、261.76%-450.09%） by significantly increasing the average weight and decreasing the volatility of individual weight（34.18%-42.64%、4.84%-32.37%）. Therefore, the“long-term deep water irrigation” mode not only ensure stable yield of rice but also improve the economic benefits of crawfish culture.