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The current study employed a combination of high-throughput sequencing and non-targeted metabolomics techniques to elucidate the changes in the quality, microbial communities, and metabolites throughout the fermentation process of traditional Midu Juanti , a traditional fermented meat product that originates from ethnic minority regions in southwestern China. The findings show that 22 dominant genera (7 bacterial and 15 fungal genera), with a relative abundance >1%, were successfully identified during the fermentation of Midu Juanti. Additionally, 979 metabolites were identified using the Human Metabolome Database (HMDB) annotation. Among these, lipids and lipid-like molecules constituted the largest proportion, followed by organic acids and their derivatives. Moreover, based on the variable importance in the projection (VIP) > 2 and P < 0.05, 60 differentially changed metabolites (DCMs) were identified. Meanwhile, the presence of Lactobacillus was positively correlated with 54 DCMs (P < 0.05, |r| > 0.5), including tryptophyl-threonine and (5R)-5-hydroxyhexanoic acid. Conversely, a negative correlation was observed between the presence of Monascus and these 54 DCMs (P < 0.05, |r| > 0.5). This study has the potential to enhance the processing theory of fermented meat products and establish a solid theoretical foundation for the control and enhancement of the quality of Midu Juanti. • Co-fermentation of plant derived and animal as raw materials of Midu Juanti. • The microbial community and metabolic characteristics of Midu Juanti was revealed. • Lactobacillus , Monascus and Pichia were dominant microorganisms in Midu Juanti. • The metabolic profile consists mainly of lipids and lipid-like molecules. • Lactobacillus , Monascus and Pichia showed strong correlation with metabolites. [ABSTRACT FROM AUTHOR]