White pepper (Piper nigrum L.), a well-known spice, is the main pepper processing product in Hainan province, China. The solid-state method of fermentation can peel pepper in a highly efficient manner and yield high-quality white pepper. In the present study, we used next-generation sequencing to reveal the dynamic changes in the microbiota during pepper peeling by solid-state fermentation. The results suggested that the inoculated Aspergillus niger was dominant throughout the fermentation stage, with its strains constituting more than 95% of the fungi present; thus, the fungal community structure was relatively stable. The bacterial community structure fluctuated across different fermentation periods; among the bacteria present, Pseudomonas, Tatumella, Pantoea, Acinetobacter, Lactococcus, and Enterobacter accounted for more than 95% of all bacteria. Based on the correlations among the microbial community, we found that Pseudomonas and Acinetobacter were significantly positively related with A. niger, which showed strong synergy with them. In view of the microbial functional gene analysis, we found that these three bacteria and fungi were closely related to the production of pectin esterase (COG4677) and acetyl xylan esterase (COG3458), the key enzymes for pepper peeling. The present research clarifies the solid-state fermentation method of pepper peeling and lays a theoretical foundation to promote the development of the pepper peeling process and the production of high-quality white pepper.