The microbial community structure associated with wine in a wine-growing region is shaped by diverse ecological factors within that region, profoundly impacting the wine flavor. In wine fermentation, fungi contribute more sensory-active biochemical compounds than bacteria. In this study, we employed amplicon sequencing to measure samples from the spontaneous fermentation process of cabernet sauvignon wines from two wine-growing regions in China to study the diversity and structural evolution of fungi during spontaneous fermentation and analyze the correlation between fungi and volatile compounds. The results showed significant differences in fungal community structure and diversity in cabernet sauvignon musts from different geographical origins, and these differences affected the flavor quality of the wines. As alcoholic fermentation progressed, Saccharomyces became the dominant fungal genus and reshaped the fungal community structure, and the diversity of the fungal community decreased. However, the fungal communities of each wine-growing region remained distinct throughout the fermentation process. Furthermore, the correlation between the fungal community and volatile compounds indicated that wine is a product of fermentation involving multiple fungal genera, and the flavor is influenced by a variety of fungi. Our study enhances the comprehension of fungal communities in Chinese wine-growing regions, explaining the regulatory role of wine-related fungal microorganisms in wine flavor.