To address agricultural green development and carbon neutrality goals, saline-alkali land remediation urgently requires a shift toward ecologically intensive pathways, but field strategies that synergistically enhance soil quality and carbon sink function in saline-alkali soils via water-saving irrigation and intercropping remain limited, particularly from the soil microenvironment driver perspective. This 4-year field study, using barren land (BL) as control, examined the effects of water management (rainfed (R) and deficit irrigation (D)) and planting patterns (wolfberry monoculture (W), alfalfa monoculture (A), and wolfberry-alfalfa intercropping (WA)) on soil amelioration, carbon turnover, and carbon sink function in saline-alkali land. Results showed that deficit-irrigated wolfberry-alfalfa intercropping (DWA) significantly improved soil water content, reduced surface soil pH and salt accumulation, and increased enzyme activities (alkaline phosphatase (ALP), catalase (CAT), urease (UE), and (3-glucosidase ((3-GC)) as well as organic carbon fractions (SOC, MBC, ROOC, and DOC) and their proportions. Compared with BL, DWA increased the carbon pool management index (CPMI) by 179.46-241.57 and enhanced carbon pool quality in the 30-40 cm soil layer. Deficit irrigation, relative to rainfed conditions, increased ecosystem respiration (ER) and gross ecosystem productivity (GEP), with DWA showing net carbon uptake. Partial least squares path modeling indicated that water management and planting patterns mainly enhanced soil carbon pool quality and carbon sink function indirectly by regulating organic carbon fractions and enzyme activities. In summary, DWA created a favorable crop root-zone microenvironment, simultaneously achieving water saving, salt suppression, soil improvement, and carbon sink enhancement, providing scientific reference for low-carbon agriculture development in saline-alkali lands of arid and semi-arid regions.