Large-scale reclamation of nabkha dunes into cropland is widespread in arid regions, yet the long-term trajectory and drivers of soil quality changes throughout deep soil profiles remain poorly understood. This study examined the vertical distribution (0-3 m) of soil quality across a chronosequence of croplands (2-5, 12-15, 25-30, and 40-50 years post-reclamation), along with bare and nabkha dunes in a desert-oasis ecotone of northwestern China. Based on soil samples collected from 100 locations using a grid-based method, a minimum data set-based soil quality index (SQI) was established. The results showed that SQI can be effectively determined using soil total porosity, silt content, soil organic carbon stock, clay content, and pH. The SQI was lowest in bare sand dunes across the entire profile, followed by nabkha dunes at 0-2 m depths (0.56-0.75). The conversion to cropland significantly (P < 0.05) enhanced the SQI, with increases ranging from 11.5 % to 126.6 % over time. This improvement was most pronounced at the 0-1 m depths, while more modest gains were also detected at deeper soil depths (1-3 m) of older croplands (25-30 and 40-50 years). Notably, pH at 0.4-3 m depths was 1.1-3.0 % higher in fields cultivated for 40-50 years than in those with 25-30 years, indicating a potential salinization risk. Spatial analysis revealed higher SQI values near water bodies, while the southeastern and mid-western nabkha dunes and bare sand dunes exhibited the lowest values. Cultivation duration was the dominant driver of SQI variation throughout the soil profile, followed by land use type, with both effects attenuating with depth. These findings demonstrate that long-term cultivation effectively enhances soil quality at 0-1 m depths in reclaimed desert soils while highlighting salinization risks in deeper layers (0.4-3 m), thereby providing a scientific basis for sustainable land management in arid agro-ecosystems.