Ginseng rusty root disease (GRRD) is one of the major diseases of ginseng, which disease is leading to a severe decline in the quality and yield of ginseng. Soil bacterial communities’ long-term survival in soil, and it plays an important role in the growth of ginseng health. To clarify the relationship between soil bacterial community and GRRD, soil properties, bacterial community structure and diversity from eight sites were analyzed. The pH value declined, GRRD was severity. Acid soils had important effect on disease occurs. The rusty root disease area of QH group from ginseng rhizosphere bacteria community richness and diversity may be significantly higher than the other groups. The community structure of eight sites soil also showed apparent differences, and the samples of each site gathered together. This study provides new insights into our understanding the relationship between the soil bacterial community and ginseng rusty root disease.