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A experiment was conducted at the Jiangxi Province Center Station of Irrigation Experiment from 2019 to 2021 to study the water and nitrogen balance under water and fertilizer regulation modes. The study aimed to propose a recommended mode for paddy fields that could save water, control pollution, reduce gas emission, and improve fertilizer use efficiency. This study examined the impact of different irrigation methods and nitrogen application levels on water saving and emission reduction in paddy fields. The experiment included six treatments, which involved two irrigation methods (intermittent irrigation and flooding irrigation, referred to as W1 and W0, respectively) and three application rates of nitrogen fertilizer (0 kg/ha, 135 kg/ha, 180 kg/ha, referred to as N0, N1 and N2, respectively). The study found that irrigation methods had a significant effect on the amount of irrigation, drainage, leakage, nitrogen load from drainage, soil nitrification potential, and ammonia volatilization. The results showed that compared to flooding irrigation, intermittent irrigation reduced the amount of irrigation, drainage, leakage and nitrogen load from drainage by an average of 25.98%, 16.03%, 8.43% and 10.86%, respectively. However, the study also found that the nitrification potential and ammonia volatilization increased by an average of 6.45% and 4.32%, respectively. Fertilization levels had a significant effect on drainage nitrogen load, early soil nitrification potential and ammonia volatilization. Compared with the treatment of N2 (180 kg N/ha), the drainage nitrogen load under the treatment of N1 (135 kg N/ha) decreased by 10.86% on average, while nitrification potential and ammonia volatilization increased by 38.74% and 3.33%, respectively. In terms of nitrogen output, the amount of nitrogen absorbed by crops was the largest, followed by the nitrogen load from field drainage, then ammonia volatilization, and then denitrification. Considering the goals of water saving, emission reduction, and the efficient utilization of water and fertilizer in paddy fields, the optimal water and fertilizer regulation mode was the W1N1 mode (intermittent irrigation combined with reduced nitrogen fertilizer application rate, 135 kg N/ha).