Panax notoginseng is a highly regarded medicinal plant that has been cultivated for more than 400 years in Southwest China. The obstacles associated with the continuous cropping of P. notoginseng are the greatest issues for the development this plant. In the present study, the micro-ecologies of soils differing in the duration of P. notoginseng planting were compared, the results of which could provide important information to aid in solving the problems associated with the continuous cropping of P. notoginseng. Soils in which P. notoginseng had grown for 1, 3 or 5 years, as well as unplanted or fallow soil, which had a P. notoginseng planting interval of 1, 3, 6 or 9 years, were collected in Yunnan Province, China. The numbers and physiological groups of microorganisms, soil enzyme activities and nutrients present in the soil were analyzed to identify the effects of continuous cropping and determine the influence of crop rotation on the soil. After P. notoginseng was planted, the ecological structure of the soil and the balance of soil nutrients changed. These changes in the soil ecosystem prevented the soil from adapting to the continuous cropping of P. notoginseng, which eventually limited the growth of P. notoginseng and increased the incidence of diseases. After rotation of P. notoginseng, some soil indicators were restored, and some indicators with irregular changes may have been caused by crop rotation and field fertilization management practices. Thus, the selection of suitable crop rotations will facilitate the use of continuous cropping for P. notoginseng.