Soil salinization poses a serious threat to agricultural sustainability in arid regions, particularly in Xinjiang, China, a major cotton-producing area. Although deep tillage and pre-irrigation are widely used for saline soil reclamation, their interactive effects on seasonal water-salt regulation and crop performance remain insufficiently understood. This study evaluated the combined effects of deep tillage depth (F1: 20 cm, F2: 40 cm, and F3: 60 cm) and pre-irrigation volume (W1: 2400, W2: 3000, and W3: 3600 m3 & sdot;ha-1) on soil salinity, soil physical properties, and cotton productivity in a saline cotton field. A two-year split-plot field experiment was conducted, and a four-stage analysis of soil salt storage was used to characterize seasonal salt transport in the 0-60 cm profile. Results showed that deep tillage was the dominant factor regulating the soil water-salt environment. Compared with F1W3, F3W3 reduced soil salt storage in the 0-20 cm layer by 32.50%. Deep tillage also improved soil physical properties, decreasing bulk density by 4.70%, increasing total porosity by 6.20%, and enhancing soil water retention by 18.30% during the growing season. The recalculated stage-based analysis showed that the greatest reduction in profile salt storage occurred during the rapid-leaching period immediately after pre-irrigation, whereas only limited net changes occurred during the growing season. By contrast, the nongrowing season was the principal period of salt re-accumulation, and this re-accumulation was clearly suppressed by deeper tillage. For cotton production, F2W2 achieved stable and relatively high yield, whereas F2W1 provided the highest water productivity, representing a 57.60-78.20% increase over F1W1. Overall, F2W2 is recommended as the most suitable treatment for balancing salinity control, crop performance, and water productivity, whereas F2W1 can serve as a practical water-saving alternative under water-limited conditions.