Abstract: Soil salinization has greatly threatened agricultural productivity and land resources in arid desert regions. The field soil improvement needs to meet the large-scale production requirements fully. Soil salinization can affect 20% of the irrigated land on a global scale, leading to a noticeable reduction in crop growth and yield. One of these regions include the Xinjiang province, China, which is located in the inland arid desert regions of Central Asia. The desert covers an area of 4.3×105 km2. The saline–alkali land area is 3.02×104 km2, accounting for 37.72% of the total cultivated land, with the annual increase of saline–alkali land accounts for 0.26%. It is a high demand to mitigate soil salinity. The impact of soil salinization can be reduced to involve water conservancy, farm management (deep-ripping, backfilling of guest soil), chemical amendments (gypsum), and biological measures (cultivation of salt–tolerant crops). The water conservancy measures include the subsurface pipe (Pa) and vertical shaft (Sa) drainage. Specifically, the Pa approach uses the surface fresh water to leach the salt from the saline–alkali soil, whereby the water enters Pa buried in the soil and flows into a drainage ditch. The Sa drainage approach uses the subsurface wells to pump out groundwater in order to effectively lower the groundwater level and discharge saline water out of the planting area. The purpose of Sa is to regulate the distribution and balance of the soil water and salt in the planting area. Previous empirical studies on soil salinization was focused mainly on the water and salt transport, physical and chemical properties of saline–alkaline soil, and technical parameters or salinization improvement. However, the Pa and Sa drainage approaches are still in the exploratory stage for the improvement of saline–alkali lands due mainly due to the secondary soil salinization. In addition, the previous studies did not provide sufficient evidence on the effect of the combined Pa and Sa drainage measures. Moreover, previous studies have focused on the 0-100 cm soil layer depths rather than the groundwater recharge on the soil salinity. In this study, a soil improvement was conducted in the five-year growing season field to evaluate the agricultural soil ecosystem under Pa and Sa drainage approaches. The main objective of this study was to evaluate the desalination and drainage effect of the drip irrigation and leaching that combined with Pa and Sa in the process of improving saline-alkali soil conditions, including the soil desalination rate, drainage flow, salt discharge, and groundwater level. This study shows that saline-alkali soils were improved to assess the effects of the combined Pa and Sa drainage measures on the agricultural soil ecosystem. The average annual decline of groundwater level from 2016 to 2020 was 1.1 m. More importantly, the seed cotton yield increased by 21%. It infers that the value of saline–alkali soil can be improved by combining the Pa and Sa drainage measures. This finding can provide a strong reference for the sustainable development of future saline-alkali soil improvement and agricultural land resource utilization for cotton production in arid desert regions.