Traditional nitrogen fertilizers (TNF), such as urea, percolate easily in arid fields, posing low nitrogen use efficiency (NUE) and a high non-point pollution risk. Controlled-release fertilizers (CRF) exhibit significantly lower deep seepage, rendering it a favorable choice in arid fields due to its ability to enhance NUE through slow-release mechanisms. However, current models do not fully account for the soil nitrogen dynamics and crop interactions under controlled-release conditions, and lack quantification. This study improved the APSIM model by adjustment the urea hydrolysis rate to assess the impact of CRF and TNF applications on soil health, crop growth, and water quality. Calibration and validation were conducted through experiments in the Hetao Irrigation District of China from 2019 to 2020, with different nitrogen application rates (135, 225, and 315 kg/ha). The model accurately simulated soil NO3-N concentration (SNC), cumulative NO3-N leaching (CNL), nitrogen uptake (NU), and sunflower yield. During the validation process, R2 and Nash-Sutcliffe efficiency (NSE) values were both above 0.75. Results indicated that the average SNC, NU, and yield under CRF application were significantly higher than those under TNF application, with increases of 38.62%, 44.92%, and 18.38%, respectively. Notably, the proportion of soil nitrogen available (PSNA), a novel metric proposed in this study, was 159.50% higher in the 0–40 cm soil layer with CRF compared to TNF. Additionally, CNL and NO3-N leaching loss rate (NLLR) decreased by 25.76% and 25.77%, respectively. Scenario simulations indicated that the optimal fertilization strategy for this region is to use 180–193.5 kg/ha of CRF with a release period of 80–85.5 d to balance agricultural productivity and ecological protection. This study confirms the significant advantages of CRF in enhancing yield, improving nitrogen management, and promoting environmental sustainability, providing a scientific basis for CRF management strategies and supporting the shift towards more efficient and environmentally friendly agricultural practices.
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