Optimizing irrigation and nitrogen (N) management in saline soils is critical for sustainable cotton production in arid regions that have been subjected to climate change. In this study, a two-year factorial field experiment (3 salinity levels × 3 N rates × 3 irrigation quotas) is integrated with the RZWQM2 model to (1) identify water–N–salinity thresholds for cotton yield and (2) to project climate change impacts under SSP2.4-5 and SSP5.8-5 scenarios (2031–2090) in Xinjiang, China, a global cotton production hub. The results demonstrated that a moderate salinity (6 dS/m) combined with a reduced irrigation (3600 m3/hm2) and N input (210 kg/hm2) achieved a near-maximum yield (6918 kg/hm2), saving 20% more water and 33% more fertilizer compared to conventional practices. The model exhibited a robust performance (NRMSE: 5.94–12.88% for soil–crop variables) and revealed that warming shortened the cotton growing season by 1.2–9.5 days per decade. However, elevated CO2 (832 ppm by 2090) levels under SSP5.8-5 increased yields by 22.6–42.1%, offsetting heat-induced declines through enhanced water use efficiency (WUE↑27.5%) and biomass accumulation. Critically, high-salinity soils (9 dS/m) required 25% additional irrigation (4500 m3/hm2) and a full N input (315 kg/hm2) to maintain yield stability. These findings provide actionable strategies for farmers to optimize irrigation schedules and nitrogen application, balancing water conservation with yield stability in saline-affected arid agroecosystems that have been subjected to climate change.
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