【Objective】Sanqi ginseng Panax notoginseng [(Burk.) F. H. Chen] is a valuable traditional Chinese medicinal herb grown in Yunnan. It is no good to cultivate the plants continuously in the same field. Reductive soil disinfestation (RSD) is a technique for pre-planting soil treatment that has been proven to be successful in overcoming the obstacles of monocropping of vegetable, flower, etc. However, it is not sure whether RSD can help overcome the obstacles of monocropping of Sanqi ginseng. Therefore, this study was designed to explore effects of RSD on obstacles in monocropping of Sanqi ginseng and growth of seedlings of the crop. 【Method】 A field experiment was carried out, designed to have four treatments, i.e. CK (control without soil treatment); SB [RSD coupled with application of 15 t•hm^-2 organic substrate high in C/N ratio, (C/N 94)]; BD [RSD coupled with application of 15 t•hm^-2 organic substrate low in C/N ratio (C/N 19)]; and SB+BD [RSD coupled with application of 15 t•hm^-2 organic substrate, containing both high and low C/N ones, half by half (m/m=1:1)]. Contents of saponins in the soils were measured with a high performance liquid chromatographer (HPLC), and microbial population and community structure were determined by means of real-time PCR and DGGE. Survival rate and disease incidence of replanted Sanqi ginseng seedlings were also recorded. 【Results】 Results show that RSD significantly helped degrade saponins as compared to CK. The degradation rate of Rb1 and Rh1 in treatments BD and SB+BD reached up to 82.1% and 85.8%~88.1%, respectively. Besides, RSD effectively reduced the population of Fusarium oxysporum (F. oxysporum) and lowered its proportion in the fungi community, with sterilizing rate reaching as high as 99.7%. Furthermore, the number of replanted Sanqi ginseng seedlings survived the transplantation for 5 months was 7.3~8.5 times higher in the RSD treatments than in CK, while disease incidence decreased significantly from 89.0% in CK to 12.9%~16.1% in the RSD treatments. 【Conclusion】Therefore, it is concluded that RSD can remarkably remove the obstacles in mono-cropping of Sanqi ginseng, improve the soil microbial community structure, raise the survival rate, and reduce the disease incidence of replanted Sanqi ginseng seedlings. So it is a promising agricultural practice to overcome the obstacles in monocropping of Sanqi ginseng.