Zanthoxylum armatum (Z. armatum) is an economic crop widely planted for both spice and medicinal purposes in Southwest China. Soil is a key environmental condition that affects seedling growth and development, and screening suitable soil types is of great significance for the large-scale cultivation of crops. This study designed growth experiments of Z. armatum seedlings in red soil (RS), yellow soil (YS), acidic purple soil (ACPS), alkaline purple soil (ALPS), and alluvial soil (AS)to screen for more suitable soil types. The growth traits of Z. armatum seedlings and the carbon (C), nitrogen (N), phosphorus (P), C:N:P stoichiometry, and non-structural carbohydrate (NSC) content of different organs were comparatively analyzed. The results showed that the morphological indexes of Z. armatum seedlings cultured in AS were better than those in the other four soils.AS and RS may be beneficial for the culture of Z. armatum seedlings due to higher nutrient levels in three organs. Two-factor ANOVA and PCA analysis showed that C, N, and P and their proportions would affect the uptake and distribution of NSC in various organs of Z. armatum seedlings. These results showed that soil types and plant organs significantly affected the accumulation and distribution of N, P, and NSC in Z. armatum seedlings. These results are conducive to screening soil types suitable for the growth and development of Z. armatum and provide data support for further large-scale cultivation of Z. armatum in suitable areas.