Abstract: Continuous cropping obstacle is a key limit factor of Panax notoginseng cultivation. The reason for continuous cropping obstacles, such as changes of soil microorganisms have not been clearly, especially under natural conditions. To evaluate the impact of P. notoginseng planting on soil microbial communities and continuous cropping obstacle mechanisms, the soil nutrients and soil microorganism community structure were investigated in different fields after different years of P. notoginseng harvested in three towns (Ganhe, A’meng and Panlong) in Wenshan City, Yunnan Province. In each town, 7 fields were selected as soil sampling sites. Seven fields were planted other corps rather than P. notoginseng, six of which were at 1 to 6 years after P. notoginseng harvested, the other one which never planted P. notoginseng was set as the control (CK). Biolog-ECO method was used to analyse the average well color development (AWCD) and diversity of microbial community to explore microbial community dynamics. The results showed that AWCD of soil microorganisms was not regularly changed with increasing years after P. notoginseng harvested. After cultivated for 96 hours, activity of soil microorganisms reached the highest level. Cluster analysis of utilization of 6 groups (31 kinds) of carbon resources showed that in three towns, carbon resources utilization of soils at 1 and 6 years after P. notoginseng harvested were classed in one group, indicting the same characteristics of carbon resources utilization. No obvious regularity was observed for other years. The use of carbohydrates, polymeric substances, carboxylic acid and phenols by soil microorganisms in 1 and 6 years after P. notoginseng harvested were 25.97%55.59% and 53.14%65.68% more than those of CK. Soil nitrogen, phosphorus, potassium and organic matter contents increased at 2 years, decreased at 4 and 5 years after P. notoginseng harvested. Soil nitrogen, phosphorus, potassium and organic matter contents in three towns, as well as Shannon-Wiener index, evenness index and Simposon’s index of soil microorganisms in A’meng and Panlong Towns at 1 to 6 years after P. notoginseng harvested were not significantly different compared with that of CK. The results suggested that rotation with other crops at least for 6 years was indispensable to avoid continuous cropping obstacles of P. notoginseng.