ContextSoil salinity stress and limited nutrient availability significantly impede crop production. Addressing these challenges, the activation of irrigation water and soil enhancement strategies have proven increasingly effective in improving crop production in saline soils. In particular, magnetized ionized water technology has been shown to augment the leaching of soil salinity, while Bacillus subtilis has been applied to increase nutrient availability. However, information on the synergistic effects of magnetized ionized water and B. subtilis are presently limited. ObjectiveThis study aimed to investigate the potential of utilizing B. subtilis in combination with magnetized ionized water to enhance cotton (Gossypium hirsutum L.) production and understand its underlying driving mechanism. MethodsA two-year field experiment explored the impact of varying amounts of B. subtilis, with two types of irrigation water [non-magnetized-ionized water (NMIW) and magnetized ionized water (MIW)] on soil conditions (pH, salt accumulation, and nutrient content), and cotton growth (dry matter, nutrient accumulation, seed cotton yield, and quality) in southern Xinjiang's saline soil. The experiment included five B. subtilis levels (0, 15, 30, 45, and 60 kg ha−1) with NMIW (designated as B0, B1, B2, B3, and B4) and MIW (designated as MB0, MB1, MB2, MB3, and MB4). ResultsMIW and B. subtilis significantly (p < 0.05) reduced soil pH and salt accumulation, while B. subtilis significantly (p < 0.01) increased soil residual nitrate nitrogen and residual available phosphorus content in the 0–40 cm soil layers compared to B0. Furthermore, a significant increase (p < 0.05) in cotton dry matter, nitrogen, and phosphorus accumulation was observed with both measures compared to B0. Seed cotton yield (Y), water productivity (WP), and fiber quality index (FQI) also showed significant improvements (p < 0.05). Compared with the NMIW treatments, the MIW treatments resulted in an average increase in Y of 5.7%, WP of 3.7%, and FQI of 20.2%. Similarly, B. subtilis treatments, compared to no B. subtilis treatments, led to an average increase in Y by 10.6%, WP by 6.9%, and FQI by 29.1%. Quadratic function relationships with Y, WP, and FQI were established using B. subtilis amount as an independent variable. The appropriate range of B. subtilis amount under MIW treatment, corresponding to 99.5% of the maximum values of Y, WP, and FQI, was determined to be 51.1–56.4 kg ha−1. ConclusionMIW and B. subtilis have been found to increase nutrient accumulation in cotton by reducing 0–40 cm soil salinity and alkalinity and increasing 0–40 cm soil nutrient content, thereby enhancing cotton production. To optimize the cotton cultivation under film-mulched drip irrigation in saline soil of southern Xinjiang, China, it is recommended to apply 51.1–56.4 kg ha−1B. subtilis under MIW.