Bozhou peony is an important herb in China known for its medicinal properties. This research specifically focuses on the Qiaocheng District in Bozhou City. The study investigates the local soil and Bozhou peony, collecting a total of 109 samples of soil–Bozhou peony combinations. The aim is to study the distribution characteristics of mercury (Hg) in the soil–Bozhou peony system and conduct a geochemical evaluation using GIS. The findings reveal that the Hg content in the soil ranges from 0.017 to 0.248 mg kg⁻¹, with an average concentration of 0.056 mg kg⁻¹. Out of the collected soil samples, 46% exhibit Hg concentrations exceeding the established soil environmental background value for mercury. The geo-accumulation index indicates Hg pollution in the study area, with slight to moderate contamination in urban areas. However, the Hg concentrations in Bozhou peony root samples vary between 0.001 and 0.004 mg kg⁻¹, all within the permissible limit set by the “Chinese Pharmacopoeia” (2020). Hg in Bozhou peony roots mainly shows weak enrichment (BCF: 0.132–0.009), and the non-carcinogenic risk associated with Hg in Bozhou peony root samples is very low. The spatial distribution of Hg in Bozhou peony is similar to that in the soil, with high concentrations of Hg found in areas where key environmental supervision enterprises are densely located. These results suggest that the enrichment of Hg in Bozhou peony is primarily influenced by the concentration of Hg in the soil.