Soil quality is a crucial attribute for maintain biological productivity, human health and ecosystem service function. However, the distribution of saline-alkali soil quality and its influencing factors in the Yellow River Delta region remain unclear, which hinders sustainable agricultural development. The study evaluated the quality of soil under different use types and depths in the southern Yellow River Delta region. We collected 134 soil samples from two soil layers at 67 soil sample points across three land use types. Spatial distribution maps revealed that inland areas exhibited better soil texture and nutrient levels compared to coastal areas. All nutrients were higher in 0-20 cm soil layer than that in 20-40 cm soil layer except soil total potassium. The spatial distribution pattern of Soil Quality Index (SQI) showed higher values at the center gradually declining towards the edge of the study area. Furthermore, SQI in cultivated land was 1.8-8% and 52.7-84% higher than that in forest land and wasteland, respectively. The SEM results indicated that distance from sea indirectly influenced soil quality with different mechanisms between two soil layers. The model in 0-20 cm soil layer, SQI was indirectly affected by chemical properties, nutrients and based ions, explained 85% of the variation in SQI. In 20-40 cm soil layer, SQI mainly effected by chemical properties explained 83% of the variation in SQI. The result could provide reference for land use, selecting suitable crops according to soil properties, which is important for promoting sustainable agriculture in the region.