Zao Chili (ZC) is a traditional fermented pepper, which plays an important role in Chinese cooking. The aim of this study was to elucidate the effect of 5-1 on the physicochemical properties, metabolite and microbiota profiling of ZC. The physicochemical factors changed regularly with the fermentation time. In the microbial communities, , , , , , and were the dominant genera. 7 kinds of organic acids were detected in the whole fermentation process of ZC, but only 5 kinds changed significantly. Based on the OPLS-DA model with VIP > 1 and ANOVA with  < 0.05, 33 volatile flavor compounds with significant differences were screened out of 89. According to the redundancy analysis (RDA), fungi mainly contributed to soluble solids, while bacteria mainly contributed to pH. , , and may be the potential flavor contributing microorganisms in the fermentation process of ZC by the Spearman correlation coefficient. A total of 11 main metabolic pathways were obtained by KEGG enrichment analysis of 89 volatile flavor compounds and 7 organic acids. Therefore, this study further enhanced our understanding of the flavor quality formation mechanism of in ZC, and providing a theoretical basis for improving the flavor quality of ZC.