(1) Background: Mianning ham is a dry-cured ham from Southwest China, known for its distinct regional characteristics and delicious taste. It is particularly favored by consumers due to its safety, as no artificial nitrites are added during processing. The microbial changes during its different processing stages significantly influence the final product's flavor. This study aims to investigate the changes in microbial communities and flavor compounds across the nine stages of Mianning ham production, from raw material preparation to salting, drying, fermentation, and maturation, using 16S and ITS sequencing, as well as solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS). The goal is to explore the correlation between these changes and provide a basis for process improvement from the initial raw material preparation. (2) Results: The microbiota of Mianning ham across different processing stages mainly consisted of Proteobacteria, Firmicutes, and Ascomycota. A total of 324 volatile compounds were identified, of which 27 were key contributors to the ham's flavor. Aldehydes contributed the most to flavor, with octanal, trans-2-nonenal, and trans, trans-2,4-decadienal being the most significant contributors at various stages. Mature Mianning ham, fermented for 1-3 years, exhibited fresh grass and earthy aromas, buttery and fatty flavors, and a distinctive roasted potato note. Correlation analysis revealed that Cobetia was the primary bacterial contributor to the main flavor compounds, especially prominent in the second year of fermentation. Among fungi, Yamadazyma and Aspergillus positively influenced several key aldehyde flavor compounds throughout the processing stages, significantly contributing to the flavor profile of Mianning ham. (3) Conclusions: Correlation analysis showed that the Mianning ham that matured for two years had the richest and most characteristic flavor. The positive and consistent impact of fungi on the ham's flavor suggests that they may warrant further research and application in Mianning ham production. This provides a theoretical basis for improving the flavor quality and enhancing the market competitiveness of Mianning ham. One of the key features of Mianning ham is its substantial accumulation of hydrocarbons, which surpasses that of hams from other regions in China. A notable characteristic of Mianning ham processing is the absence of artificially added nitrites as antioxidants and color fixatives. Whether this absence is a contributing factor to the significant accumulation of hydrocarbons warrants further investigation.