[Objective] The environmental background of parent rock and soil of Paeonia szechuanica was studied in order to provide a theoretical reference for understanding the supergene geochemical behavior of nutrient elements and the role of microorganisms in elements migration. [Methods] The contents of nutrient elements (P, S, K, Ca, Na, Mg, Al, Fe, Mn, Cu) in the parent rocks, soil and the seeds of Paeonia szechuanica were measured by using ICP-OES. Meanwhile, the composition and structure of bacteria and fungi in the rhizosphere microorganisms were analyzed by using the Illumina platform. [Results] ① The soil of Paeonia szechuanica was characterized by alkalescence and rich calcium, and the element composition basically retained the characteristics of parent rock. ② The migration coefficients of elements migration from rocks into soil were listed as: Ca > Na > S > P > Mg > K > Al > Fe > Mn > Cu, and the absorption coefficients were listed as: P > S > K > Cu > Mg > Ca > Na > Mn > Fe > Al. ③ The leaching index of alkali metals and the ratio of Al to Fe shwowed a significant effect on soil bacterial diversity (Alpha), but not on fungi. ④ The migrations of P and Mn were mianly controlled by the parent rock, while the migrations of Fe, S, Mg, K, and Ca were affected by microorganisms. [Conclusion] The bacteria and fungi play similar roles in the elements migration system and mainly involve in the reaction process of Fe, S, Ca and Mg.