Abstract: To investigate the microbial community structure and flavor quality of traditional Tibetan fermented milk, high-throughput sequencing and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME–GC–MS) were used to analyze the microbial diversity and volatile flavor components in traditional Tibetan fermented milk. The types and contents of organic acids were determined by liquid chromatography. The results showed that the main dominant bacterial flora in traditional Tibetan fermented milk products were Lactobacillus, Streptococcus, and Lactococcus, etc., while the main dominant fungal flora were Saccharomyces, Kluyveromyces, and Geotrichum, etc. Six organic acids were identified, including acetic acid, citric acid, lactic acid and so on, among which, lactic acid was the most abundant (6989.02 mg/L), followed by acetic acid (1047.25 mg/L). A total of 35 volatile flavor compounds were detected in the fermented milk, with esters accounting for the highest proportion (43.98%), followed by alcohols (28.98%) and acids (16.00%). The composition and concentration of volatile flavor compounds in fermented milk exhibited notable regional variations. Fermented milk from Shigatse was distinguished by pronounced fruity aromas, particularly pineapple and banana, complemented by creamy notes, which together contributed to a rich and complex flavor profile. By contrast, fermented milk from Nagqu was characterized by strong creamy aromas, nutty undertones, and a balanced sweet–sour taste, whereas fermented milk from Ali demonstrated a predominance of more intense fruity aromas. Spearman’s correlation analysis based on key odor–active compounds (odor activity value, OAV>1) revealed distinct associations between microbial taxa and flavor compounds. The bacterial genera most strongly correlated with key flavor compounds were primarily Lactobacillus, Acetobacter and Leuconostoc, while the fungal genera most closely linked to flavor development included Apiotrichum, Dipodascaceae and Pichia. This study elucidated the correlation between microbial community structure and the formation of aroma compounds in traditional Tibetan fermented milk, providing a theoretical foundation for the standardized production, targeted flavor regulation, and development of functional strains for traditional dairy products.