Soil salinization impacts over 6 % of the world’s arable land, presenting an even greater challenge to agriculture in arid regions. This s
Soil salinization impacts over 6 % of the world’s arable land, presenting an even greater challenge to agriculture in arid regions. This study assessed various subsurface pipe arrangements (B1: 1.0 m depth, 20 m spacing; B2: 0.8 m depth, 16 m spacing), deep vertical rotary tillage (DVRT) depths (DT40: 40 cm, DT60: 60 cm), and conventional tillage (CT) over the period from 2021 to 2023 to evaluate their long-term effects on soil properties, drainage characteristics, and crop production. The results indicated that the combination of DVRT and SPD significantly reduced the levels of salt and ions (Na+, K+, Mg2+, Ca2+, Cl−, and SO42−). Increasing tillage depth and reducing pipe spacing and depth significantly improved soil desalination and drainage but reduced soil water storage. Meanwhile, the total nitrogen (TN), phosphorus (TP), and potassium (TK) contents in the 0–20 cm soil layer were significantly reduced by 3–8 %, 3–6 %, and 9–19 %, respectively, compared to the CT treatment. Specifically, the DT60-B1 treatment exhibited the greatest soil desalination and drainage but also had the highest concentrations of TN, TP, and TK in the drainage. Although these changes initially caused a 5 % and 8 % decrease in average dry mass and yield, respectively, cotton’s uptake of Na+ and Cl− decreased over time, while the uptake of Ca2+, as well as the accumulation of C, N, P, and K, along with yield, gradually increased. Random forest analysis showed that soil salinity and water storage significantly impacted yield, with electrical conductivity identified as the primary limiting factor. In 2023, the DT60–B1 treatment yielded significantly more than the CT treatment, and its comprehensive evaluation index increased from 0.44 to 0.67, indicating a shift from inhibition to promotion of crop growth over time. Long-term application requires optimizing pipeline layout and farming practices to improve productivity and sustain saline soil use.