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Large-scale vegetation restoration has been performed to improve the fragile ecological environment of the Loess Plateau in the last decades. At present, the effects and mechanism of long-term vegetation restoration on soil properties in ecosystems require further exploration to provide a reference for rational ecological construction. Hence, we investigated the differences in vegetation attributes and soil properties between three typical vegetation types (Pinus tabulaeformis plantation forest, PTPF; Robinia pseudoacacia plantation forest, RPPF; natural secondary forest, NSF) after long-term (30–40 years) vegetation restoration in the western Loess Region, China. Our results showed that (1) the arborous synusia biomass of the plantation forests was twice that of NSF, whereas NSF had almost 50% higher near-surface synusia biomass than the plantation forests; (2) the soil nutrient contents of the plantation forests were lower (30%) than those of NSF; (3) the soil bulk density, organic matter, total nitrogen, and phosphorus were positively related to arborous and shrub synusia biomass; (4) the coupling effects of four biological synusiae (with the contribution of 47.67%) were the dominant factors affecting soil physicochemical properties. Natural forests have the better vegetation attributes and soil properties than plantation forests, indicating that the close-to-nature restoration should be considered in ecological restoration. These findings can provide scientific support and theoretical basis for reforestation and ecological restoration in the Loess Plateau region and similar areas in the future.