To elucidate the effects of biochar addition management practices under different water and fertilization on the stability of saline soil aggregates and organic carbon (SOC) in the Tarim River Basin, a five-year field experiment was conducted from 2019 to 2023 to investigate the effects of biochar combined with different irrigation and nitrogen fertilization treatments on soil aggregate structure and its SOC distribution, which included seven irrigation and nitrogen fertilizer treatments: (CK: N 0 kg/hm²+0 mm water, LNLW: N 100 kg/hm²+140 mm water, MNMW: N 200 kg/hm²+220 mm water, HNHW: N 300 kg/hm²+ 320 mm water), with corresponding biochar-amended treatments (LNLWB, MNMWB, HNHWB, 10 t/hm² biochar addition). Aggregate compositions and associated SOC contents were analyzed using wet and dry sieving methods. The results showed that: 1) Compared with CK, the addition of biochar significantly improved soil aggregate stability, increased water-stable macroaggregate content by 117%, increased mechanically stable large macroaggregate content by 11%, and decreased percentage of aggregate destruction (PAD) by 8%. In the treatments without biochar addition, soil aggregate stability decreased and PAD increased with increases of water and nitrogen inputs; 2) Biochar application significantly promoted SOC accumulation in aggregates, compared with non-biochar treatments, SOC in water-stable macroaggregates, mechanically stable large macroaggregates, and whole soil increased by 1.0-5.0, 2.4-4.0 and 1.2-1.5 g/kg, respectively, with amplification effects intensifying under higher water-nitrogen inputs; 3) Wet sieving demonstrated superior sensitivity in characterizing aggregate stability-SOC correlations in saline-alkali soils compared to dry sieving, recommending its prioritization in similar studies. This research offers insights into synergistic irrigation-nitrogen-biochar management strategies for enhancing saline soil structure and improving carbon sequestration efficiency in arid regions.