Drought severely impacts crop productivity and fertilizer efficiency in arid regions, hindering sustainable agriculture. Enhancing plant drought tolerance and fertilizer efficiency is crucial for adaptation. Bacillus subtilis can improve soil structure and rhizosphere activity, boosting nitrogen utilization and crop yields. This study investigates Bacillus subtilis' potential to mitigate drought stress and enhance cotton growth, aiming to establish a water-bacteria interaction-based irrigation model. Cotton (Tahe 2), the popular variety in local, was selected as the experimental crop, and planted in test pits (3.3 mx2 mx3 m) under varying Bacillus subtilis rates (0 kg center dot ha-1 and 45 kg center dot ha-1) and drought stress -levels (H for conventional irrigation, 350 mm and L for 80 % of conventional irrigation, 280 mm). Each treatment has three replicates. The results showed Bacillus subtilis increased soil water retention by 1.07 %-33.08 % and nitrogen use efficiency by 8.94 %-9.28 %. Cotton growth was also improved, with plant height increasing by 6.45 %-10.5 %, stem diameter by 1.2 %-10.5 %, and leaf area index by 5.3 %6.97 %. Photosynthesis was enhanced, with leaf internal water use efficiency up by 1.02 %-4.21 % and instantaneous water use efficiency by 0.33 %-9.7 %. Yields increased by 8.94 %-9.28 %, and water use efficiency by 5.49 %-19.22 %. Furthermore, bacterial network analysis and the neutral community model revealed that Bacillus subtilis altered the microbial community and rhizosphere environment, increasing the complexity of the bacterial network. This optimized the availability of water and nutrients for root uptake, enhanced the biological utilization of carbon and nitrogen, and supported microbial metabolism and plant growth. These effects reduced the adverse impact of drought stress, alleviated environmental pressures, and fostered a healthier and more sustainable soil ecosystem. In conclusion, combining deficit irrigation (280 mm) with Bacillus subtilis (45 kg center dot ha-1) can effectively alleviate water scarcity and increase cotton yield in arid regions, providing valuable insights for sustainable agricultural development.