The contradiction between land improvement in saline-alkali areas and water-saving irrigation in the arid regions is becoming increasingly prominent, affecting the movement of soil water and salt as well as cotton growth. To effectively improve soil quality and alleviate soil salinization issues under the premise of water conservation to increase cotton yields, a method involves conducting brackish water leaching during the non-growing season and utilizing freshwater drip irrigation during the growing season for cotton under subsurface drainage. A 2-year field experiment using six subsurface drainage systems at different depths of 0.8 and 1.1 m and different spacings of 10, 20, and 30 m respectively, alongside a non-drainage treatment as control (CK) was conducted in Aral, Xinjiang, China. Furthermore, efficient simulations of soil water and salt dynamics as well as cotton growth in arid regions under subsurface drainage conditions could be achieved using AquaCrop and DRAINMOD-S models. The results showed that soil salinity leaching could be achieved effectively with the use of appropriate brackish water and subsurface drainage pipes with the proper technical parameters during the non-growing season. Compared with the non-drainage treatment, the subsurface drainage and drip irrigation with freshwater reduced soil salinity effectively and improved growth indices and cotton yield considerably during the growing season. The rate of soil desalination exhibited an upward trend as the distance of subsurface pipes decreased, and the growth indices of cotton increased with the decrease in distance and depth of t subsurface pipes. This study concluded that using brackish water in the non-growing season, appropriate selection of irrigation water volume, spacing, and depth of subsurface pipes can simultaneously improve soil salinity drainage and cotton yield. This research suggests new irrigation and management recommendations for agricultural production and achieves more efficient water use and crop cultivation under arid conditions, providing a new insight into the efficient use of saline soil resources in the arid regions in Xinjiang.