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Phellodendron chinense is an extraordinary medicinal plant, and its stem bark is a famous traditional Chinese medicine in China, containing a number of phytochemicals with biological and pharmacological functions. Studies have shown that the medicinal ingredients in P. chinense from various regions are different, as soil types might be important factors affecting the growth and quality of P. chinense. In this study, the effects of acidic purple soil, alkaline purple soil, yellow soil and red soil on the growth, nutrient element accumulation and partitioning in P. chinense seedlings were studied. Our results showed that the biomass of leaves and stems in acidic purple soil was significantly higher than in other soils, and the root biomass was significantly lower than that in yellow soil. C, N, P and Ca contents cultured in acidic purple soil were the highest compared to other soils, and K and Mg content were the highest in yellow soil and red soil, respectively. The distribution of carbon between different organs can reflect environmental stress. N has become a limiting factor for the growth and development of P. chinense seedlings. C:N and C:P ratios in the leaves were significantly lower than those in the stem and roots. Among four soil types, the highest N:P ratio was 1.65 in P. chinense seedlings. These results suggest that four soil types may significantly affect the accumulation and distribution of biomass and nutrient elements in P. chinense seedlings. The characteristic patterns in different organs have different responses. Acidic purple soil is more suitable for the growth of P. chinense. These findings will help to understand the distribution characteristics and requirements of nutrient elements in P. chinense seedlings, and further provide a theoretical basis and reference for site selection and cultivation strategy.