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Soil nutrients in deep soils are important for nutrient cycling and plant growth. Organic amendments have been widely used for enhancing soil health and crop yield. However, little is known about the effects of organic amendments on the vertical distributions of soil nutrients. Based on a 32-year long-term organic amendment experiment, the objective of this study was to evaluate changes in the vertical distribution of nutrients in a soybean–wheat system Vertisol. The results showed that NPK with manure or straw application significantly increased soil organic carbon (SOC), total N, total P, alkali-hydrolyzable N, available P and available K above the 40 cm soil layer. Variations in soil micronutrients primarily occurred above the 20 cm soil layer, and the highest contents were observed for NPKWS and NPKPM, respectively. Nevertheless, large amounts of NO3−−N contents accumulated in the 120–200 cm depth with manure but not straw application, indicating a high potential risk of nitrate leaching in manure treatments. These findings suggested that the application of organic amendment (manure or straw) could be recommendable for improving soil nutrients along the soil profile. Straw incorporation could be used as an alternative option for sustainable agriculture in regions with inadequate manure resources or severe nitrate leaching. [ABSTRACT FROM AUTHOR]