Soil salinization has seriously affected crop growth and fertilizer utilization efficiency in agricultural production, thus restricting the food production and sustainable development of agriculture in arid areas. Therefore, how to improve the saline-alkali land improvement and fertilizer utilization efficiency will directly affect agricultural development in arid areas. Bacillus subtilis had certain advantages in saline-alkali land improvement by inhibiting the accumulation of excessive sodium and improving the absorption of nutrients by crops. So this study proposed to use the functional advantages of Bacillus subtilis in the root layer soil, and establish a bacteria-fertilizer coupling improvement strategy to improve cotton growth and soil nitrogen use efficiency under salt stress. In this study, the physiological characteristics of crops under different soil salt stress were analyzed by pot planting cotton. Four application amounts of Bacillus subtilis agent (2.5, 5.0, 5.0 and 10.0 mg center dot kg(-1)) and three application amounts of nitrogen fertilizer (150, 300 and 450 kg center dot hm(-2)) were applied in four kinds of soil with different salinity (nonsalinized, mildly salinized, moderately salinized and severely salinized). Through the 3414 exper-imental design method, a total of 15 cross-treatments were set, including blank control. And three groups of control repetition were set in the experimental design. The results showed that the application of Bacillus subtilis improved the water retention and nitrate nitrogen retention of saline-alkali soil. When the application amount of nitrogen fertilizer was 300 kg center dot hm(-2) and the application amount of Bacillus subtilis agent was 5.0 mg center dot kg(-1), the growth index (plant height, stem diameter, and biomass) of cotton reached the maximum value. Malondialde-hyde content increased with the increase of soil salt content, which showed salt stress could cause oxidative damage to leaves. Application Bacillus subtilis agent promoted the activity of Peroxidase and Catalase enzymes in leaves and protected plants against the damage caused by salt stress. The application of Bacillus subtilis agent and nitrogen fertilizer could improve the physiological activity of leaves and reduce oxidative damage under salt stress. According to the cotton yield, the coupling application of Bacillus subtilis agent and nitrogen fertilizer significantly increased the dry matter accumulation and final yield of cotton. Compared with the control treatment, the cotton yields of Bacillus subtilis agent and nitrogen fertilizer applications treatments increased by 10.47-65.52%, which has a positive effect on improving the cotton yield in saline-alkali soil. Based on the above results, this study could serve as a theoretical basis for harnessing saline-alkali land and promoting sustainable development of agriculture in arid regions.