Bats are a potential reservoir of zoonotic pathogens. Some strains of bacteria in the gastrointestinal tract of bats are pathogenic to humans. Hypsugo alaschanicus feeds on insects and has a wide geographic distribution in China, and people are in frequent contact with these bats. However, assessing the gut microbiota, especially the potential pathogens, is needed for public health. Thus, this study aimed to explore the microbial diversity of the gastrointestinal tract of H. alaschanicus and to estimate the risk to humans caused by the hosted pathogenic bacteria. The 16S rRNA gene V1−V2 regions were sequenced using MiSeq high-throughput sequencing platform to study the bacterial community of both the stomach and the intestine of H. alaschanicus. A total of 21, 336 and 34, 188 high quality reads of microbiota were obtained from the stomach and intestinal tract of H. alaschanicus, respectively. The phylogenetic analyses showed that the gastrointestinal bacteria were mainly classified into five phyla, dominated by Proteobacteria (27.8% in stomach and 39.7% in intestine) and Firmicutes (59.5% in stomach and 12.7% in intestine). Enterococcus and Bacillus were the two dominant bacterial genera in the stomach, accounting for 46.1% and 7.4% of total bacteria, respectively. Sphingomonas and Mycobacterium were the two dominant genera in the intestine, accounting for 10.5% and 7.3% of total bacteria, respectively. Furthermore, the results revealed that H. alaschanicus carried a large number of human pathogens and thus should be the subject of greater study to prevent transmission of diseases from bats to humans.