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Rice production is intimately related to water and nitrogen management, whereas rice yield inevitably decreases with extreme rainfall. Optimization of water and nitrogen management may mitigate the degree of rice yield reduction. Hence, we conducted a field experiment in a normal and wet year to investigate suitable water and nitrogen management that could reduce the risk of rice yield reduction. The field experiment comprised six water and nitrogen management methods, which included two irrigation methods (CF: continuous flooding; AWD: alternating wet and dry) and three nitrogen fertilizer levels (N0, N90, and N180: 0, 90, and 180 kg N ha−1, respectively). The results showed an average yield reduction of 23.5% in the wet year compared to normal year. The nitrogen rate of N0, N90, and N180 resulted in a 36.9%, 24.8%, and 11.0% of yield reduction in the wet year, which presented a decrease in yield reduction with the increase in nitrogen rate. Panicle contributed over almost 60% and 75% on average to biomass and total nitrogen uptake, but both the total amount and proportion of nitrogen uptake in panicle showed a decrease in the wet year. In addition, the rice yield showed a significant positive correlation with nitrogen uptake both in the normal and wet year. Therefore, in the wet year, the decrease in nitrogen uptake in panicle results in a yield reduction. With the increase in nitrogen rate, the nitrogen internal use efficiency (IEN) was significantly decreased in the normal year, while it increased in the wet year, and the nitrogen recovery use efficiency (REN) and nitrogen harvest index (HIN) were not affected by nitrogen rate. Therefore, these results suggested that increased nitrogen rate in a wet year could improve rice nitrogen uptake to reduce the risk of yield reduction and maintain the nitrogen use efficiency (NUE).

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