Objective: This study focuses on ensuring qualified bacterial indicators during betelnut processing. Methods: The key processing samples from the raw material to the finished product were analyzed by the Illumina Miseq high-throughput sequencing technology. Results: The results showed that a total of 191 456 effective sequences were obtained from the 7 kinds of betelnut samples, belonging to 790 genera, 239 families. The dominant bacteria genera include Bacillus, Pseudomonas, Hydrogenophaga, Leuconostoc, and Chryseobacterium. Significant differences in the bacterial community structure was found in the betelnuts between before and after storage. The species richness in betelnuts before storage (new betelnut) was higher than those after storage (old betelnut), while the bacteria in the old betelnut had higher species diversity. During the processing, the boiled betelnut process and the process from cut betelnut to product betelnut could effectively kill bacteria. The number of extinct bacteria genera in the two stages was 216 and 227 respectively. The process from boiled betelnut to stuffy fragrant betelnut was susceptible to bacterial contamination in the environment, and the number of new bacterial genera was 126. Conclusion: The variation of the polluting bacteria diversity during betelnut processing indicated that the control and prevention of pollution should focus on bacterial proliferation in the pickling and flavoring process, as well as the environmental pollution in each process. The key to reducing bacteria is to make good use of the boiling and the process before product finished.