The study aimed to explore the bacterial community composition and the functions of core microbiota inEucommia ulmoidesbark. The bark samples ofE. ulmoideswere collected from Wangcang Sichuan Province, Cili Hunan Province, and Zunyi Guizhou Province, in China, respectively. Through the high-throughput sequencing methods and techniques, the community composition, core microbiota, and function of the bacteria were studied. The bacterial community ofE. ulmoidesbark consisted of 9 phyla, 11 classes, 22 orders, 28 families, 31 genera, and 37 OTUs. At the genus level, the dominant genus was the unclassified bacteria of Cyanobacteria, with a relative abundance of 97.01%. The bacterial communities ofE. ulmoidesbark from different areas have their unique units except for the common microbiota. The core microbiota of bacteria included an unclassified genus of Cyanobacteria, an unclassified genus of Mitochondria,Pseudomonas,Sphingobium,Rhizobium,Novosphingobium,Enterobacter,Rhodococcus,Curtobacterium,andRalstonia. FAPROTAX function prediction suggested that the core microbiota has a substantial potential for photoautotrophy, phototrophy, aerobic chemoheterotrophy, chemoheterotrophy. Ten taxa composed the core microbiota, and the majority of them were related to the pharmacologically active ingredients ofE. ulmoidesbark. The research provides a scientific basis for the biological marker of genuineness and microbial technology for improving the content of medicinal ingredients ofE. ulmoides.