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The research on the effect of water-saving irrigation technology on the loss of nutrients and chemical substances in farmland has become a hot issue in the field of agricultural water and soil. Based on comparative experiments and combined with the isotope N¹⁵ tracer technique, the mechanism of nitrogen migration and transformation and the trend of fertilizer nitrogen use under different irrigation modes were studied. The results showed that water-saving irrigation modes (thin and wet irrigation W1 and intermittent irrigation W2) could reduce the NO₃^−-N leaching loss by reducing the water leakage amount and the NO₃^−-N concentration, and effectively inhibit the leaching loss of fertilizer nitrogen. Compared with conventional irrigation (W0), the leaching loss amount of fertilizer nitrogen in W1 and W2 decreased by 62% and 64%, respectively. Under the same amount of fertilizer, water-saving irrigation mode can significantly reduce the total amount of ammonia (NH₃) volatilization and the proportion of NH₃ volatilization of fertilizer nitrogen in total NH₃ volatilization, and significantly increase the nitrogen uptake of rice plants. Meanwhile, water-saving irrigation mode can increase the total nitrogen content of paddy soil by 14.0% but reduce the residual rate of fertilizer nitrogen in soil by 14.6%. Moreover, crop nitrogen uptake can be significantly increased under water-saving irrigation. Compared with W0, the nitrogen fertilizer use rate of W1 and W2 increased by 5.0% and 9.7%, respectively. The research results can provide an important basis for controlling agricultural non-point source pollution, curbing the decline of soil fertility and deterioration of soil quality in paddy fields.