Petit Verdot is widely used in blend wines but only few studies focus on the effect of microorganisms on the aroma formation of its monovarietal wine. This study explored the correlation between microorganisms and aromas during spontaneous fermentation (SF) and inoculated fermentation (IF). The changes of volatile compounds and microbial succession during the wine fermentation were monitored by HS-SPME-GC-MS and HTS. The results showed that SF resulted wines with more aromatic and regional characteristics because of significantly higher content and varieties of higher alcohols, acetate esters and C6 compounds, thus highlighting the ‘floral’ and ‘fruity’ characteristics of Petit Verdot wine. The PCA and OPLS-DA showed that there were significant differences in aromas and microorganisms under SF, and IF, while correlations between them were established by OPLS and Spearman (VIP >1, P < 0.05). Among them, four unique core bacteria in SF were positively correlated (P < 0.05) with four important higher alcohols and most of the esters. Non-Saccharomyces in SF were positively correlated (P < 0.01) with C6 compounds. Therefore, SF had a potential application prospect for improving wine flavor and provided a reference for further understanding the role of microorganisms in the formation of aroma compounds.