Addressing challenges arising in saline alkali soils is very important in enhancing crop productivity particularly in arid and semi-arid lands. Drip fertigation, which is an integrated form of water and nutrient management, appears to be a promising solution to the problems of water scarcity and soil salinization. While short and medium-term research has focused on its positive effects, its long-term impact on the soil and thus the sustain crop production and soil ecosystem functions, especially the interactions between soil water-salt balance, microbial processes, and crop yield, is poorly explored. This study examines the long-term (12-27 years) effects of drip fertigation in saline-alkali cotton fields in Xinjiang, China, with adjacent uncultivated saline-alkali wasteland (SWL) as the control. Results show great improvements in soil physical properties, including reduced salinity (SSC from 8.29 g kg-1 to 0.55-1.50 g kg-1) and pH (from 8.29 to 7.26-7.61), and improvement in soil porosity (SP), bulk density (BD) and water content (SWC), especially in the 0-40 cm root-zone. Soil structural stability was increased and the results showed the higher water-stable aggregates (R0.25), mean weight diameter (MWD), and geometric mean diameter (GMD). Furthermore, soil carbon (SOC, DOC, MBC) and nitrogen (TN, NH4+-N, NO3--N) pools resulted in the significant increases following the enhanced nutrient cycling and microbial activity. Machine learning (Random Forest) and structural equation modeling (PLS-SEM) showed effects of better soil structure and reduced salinity to increase the cotton yield from 5272.36 kg ha-1-6101.95 kg ha-1. This study emphasizes the transformative potential of using long-term drip fertigation to improve the functioning of the soil-plant system, improve the resource use efficiency and increase crop productivity in saline alkali areas in water deficient condition.