Soil organic carbon (SOC) serves as the principal carbon reservoir in terrestrial ecosystems, significantly influencing soil quality and ecological processes. Typically characterized by slow mineralization rates and low external carbon inputs, saline soils generally exhibit low SOC storage. However, the effect of soil salt accumulation on SOC stability in hyper-arid desert ecosystems remains poorly understood. This study employed the halophyte Caligonum caput-medusae (Calligonum) in a 3-year pot experiment with three NaCl concentrations (1, 2, 3 g kg-1) and a control (CK, 0 g kg-1) at the Taklimakan Desert's southern margin. We analyzed topsoil (0-30 cm) and subsoil (30-80 cm) properties including organic carbon fractions, iron/aluminum oxides, microbial properties, and microbial carbon use efficiency (CUE). Results revealed that NaCl treatment (>= 1 g kg-1) inhibited Calligonum growth, reduced the activities of soil beta-1,4-glucosidase, cellobiohydrolase, and leucine aminopeptidase, as well as particulate organic carbon (POC) accumulation compared to the control. Conversely, NaCl treatments enhanced mineral-associated organic carbon (MAOC) by 7.9%, microbial CUE by 6.1%, and SOC by 3.4% compared to the CK. Across all treatments (>= 0 g kg-1), topsoil POC exceeded subsoil levels by 6.0%. Further analysis identified MAOC as the primary SOC driver, followed by POC and microbial properties (including microbial CUE). Overall, this study determined that 3 years of salt treatment did not exacerbate SOC loss; instead, MAOC accumulation coupled with elevated microbial CUE increased SOC stability. These findings provide a "carbon" erspective for the selection of Calligonum as vegetation restoration in desertification control under different salt-affected conditions.