[Objective] To explore the structure, function and relationship of bacterial community in sclerotia, cortices and habitat soil of Cordyceps cicadae under the natural ecology. [Methods] High-throughput sequencing of bacterial 16S rRNA amplification fragments was performed to analyze the composition, diversity and potential functions of bacterial community in sclerotia, cortices and habitat soil of Cordyceps cicadae in Mount Dajiang and Guiyang Forest Park. [Results] A total of 562 bacterial genera were detected in the sclerotia samples, 521 genera were detected in the cortices samples, and 578 genera were detected in the hyphosphere soil samples. The bacterial community structure of each group of samples from the two places was similar. In the sclerotia samples, Pseudomonas and Sphingobacterium were the dominant populations. Pseudomonas and Aminobacter were the dominant populations in the cortices samples. The norank_c_Acidobacteria and norank_f_Xanthobacteraceae were the dominant genera in the soil samples. Venn analysis showed that the hyphosphere soil samples included most genera of the cortices samples, and the sclerotia samples had more endemic genera, such as Wolbachia and Rickettsia. Furthermore, the PICRUSt function prediction results showed that there are a total of 24 gene function families, which are mainly related to the metabolism and transportation of material and energy, as well as the occurrence and regulation of cell behavior. [Conclusion] Bacteria in the Cordyceps cicadae and its microhabitat had rich diversity. Their potential function may be related to the metabolism of nutrients and played important roles in the individual growth and development of the Cordyceps cicadae. The results have reference value for supplementing the ecological information data of Cordyceps cicadae and imitateing wild cultivation.