Soil salinization hinders cotton (Gossypium hirsutum L.) production and sustainable agricultural in arid regions. In this study, the effects of deep vertical rotary tillage (DVRT) on soil moisture, temperature, salinity, root system, cotton photosynthetic characteristics, and yield were evaluated over a two-year experiment. Two tillage methods were implemented: conventional tillage (CT, 0.20 m depth) and DVRT at 0.20, 0.40, and 0.60 m depths. Three treatments were evaluated: (i) continuous CT, (ii) alternating DVRT (DT20, DT40, DT60) with CT, and (iii) continuous DVRT (CDT20, CDT40, CDT60). Deep vertical rotary tillage (DT and CDT) increased soil moisture, reduced electrical conductivity, regulated soil temperature, enhanced cotton photosynthesis, root boll capacity, and ionic balance (Cl-, Ca2+, and Na+ uptake). Among all treatments, DT60 showed the best yield response, increasing yield by 47 % and 44 %, improving fiber quality index by 35 % and 32 %, and enhanced water use efficiency (WUE) by 45 % and 50 %. Although CDT treatments enhanced salt leaching, they reduced soil moisture in bare ground more significantly than in mulched areas, indicating that excessive tillage increases evaporation, reduces water retention, and inhibits root development, thereby lowering WUE. The partial least squares path model revealed that DVRT optimized soil conditions, promoting root development and photosynthetic efficiency, thereby supporting biomass accumulation and yield formation The random forest model showed that soil moisture was the primary factor for yield formation, emphasizing its role in saline agriculture. These results highlight the importance of regulating soil moisture to improve crop yield, resource efficiency, and address climate change.