Panax notoginseng is a traditional valuable Chinese medicine plant that can be used for the treatment of cardiovascular diseases, inflammation, trauma, and hemorrhage. In recent years, the heavy metal pollution problem of P. notoginseng has attracted widely attention, however studies on this regard are limited. In this study, the heavy metal pollution of P. notoginseng and soil in Wenshan (Yunnan, China) was investigated; the bioaccumulation and transfer of heavy metal in P. notoginseng was revealed; and the associated health risk was evaluated. Concentrations of Cd, Cr and Cu in soil samples fell in the ranges of 0.13-1.87 mg/kg, 71.35-273.73 mg/kg and 13.96-86.16 mg/kg, respectively. Cd concentrations in 75%, Cr concentrations in 38%, and Cu concentrations in 50% of the soil samples exceeded the Environmental Quality Standard (GB15618-1995), indicating that serious pollution existed in P. notoginseng planting area. Shapiro-Wilk test revealed that concentrations of soil Cd, Cr and Cr were not normally distributed (The P values of Cd, Cr and Cu were 0.004, 0.02 and 0.03, respectively, which were lower than 1), indicating that human activities had caused skewed probability distribution. Nemerow index analysis indicated that the magnitude of pollution followed the order of, from high to low, Qiubei, Wenshan, Yanshan and Maguan county. The concentrations of Cd, Cr and Pb in P.notoginseng were 0.23-5.50 mg/kg, 0-30.57 mg/kg and 0.12-27.45 mg/kg, respectively. and approximately 81%-100%, 75%-100%, and 25%-63% of the herb samples exceeded the Green Standards of Medicinal Plants and Preparations for Foreign Trade and Economy (WM/T2-2004) or NSF International Draft Standard (173-2001).Bioaccumulation factors (BCF) of Cd, Cr, Cu and Pb were 1.51-4.01, 0.01-0.11, 0.13-0.37 and 0.11-0.37, respectively in different part of P. notoginseng. Transfer factors (TF) of Cd, Cr, Cu and Pb were 1.23, 0.41, 1.14 and 3.61, respectively in P. notoginseng. Different parts of P. notoginseng accounted for 13.46%-46.40%, 8.67%-24.67% and 1.90%-14.40%, respectively, of the ingestion rates with ADI (Allowable Daily Intake). The correlation coefficient between heavy metal concentration in soil and the percent of main root ingestion rates with ADI were 0.841^** (Cd), 0.789^** (Cr) and 0.753^** (Cu) (The double-asterisk is used to represent P < 0.01), respectively. This means that the health risk of Cd, Cr and Cu in the main root of the herb increased with the increasing metal concentrations. In conclusion, heavy metal pollution of soil and P. notoginseng in the planting area of Wenshan should not be neglected, and effective measures should be adopted to reduce heavy metal accumulation in the herb and human health risks.