Abstract: Soil samples of Gastrodia elata planted in different years were collected from Qiaoshan Town, Yiliang County, Zhaotong, Yunnan Province. The sample names and numbers were recorded in the book. Three groups were selected to analyze the bacteria changes in community structure and differences in species abundance among the original soil, a crop soil of G. elata planting soil and bamboo soil by high throughput sequencing technology. The results showed that the endemic bacteria OTU in the original soil was higher than bamboo soil and a crop soil; compared with the original soil, the endemic bacteria and the abundance of dominant bacteria decreased significantly after planting and harvesting; the number of endemic bacteria in the soil was restored based on the restoration experiment of bamboo planting, which indicated that the bacterial community structure in the soil of G. elata may be restored by rotation of local commercial crop bamboo.