The main pollutant accumulation and microbiological characteristics changes in soils with different notoginseng- planting years were investigated and analyzed. The results showed that the contents of all heavy metals, Zn, Cr, Cd, As, Ni, Hg and Cu exceeded the national soil environment quality standard, and the pollution levels of As and Cd were the most serious. With the increase of notoginseng-planting year, the contents of Cu and Cr in soil increased. Pentachloronitrobenzene and chlorpyrifos remained in the soils and the average contents were 42.6 μg/kg and 79.4 μg/kg, respectively. With the increase of notoginseng- planting year, the utilization of carbon sources by soil microbial communities was enhanced, the uniformity of microbial species changed, the activities of soil dehydrogenase and urease increased first and then decreased. Redundancy analysis showed that As and Ni inhibited microbial activity and diversity.