Display omitted •Initial fungal diversity positively impacted fungal succession.•Fungal succession significantly affected metabolic succession.•Metabolic succession drove metabolic diversity.•Initial fungal diversity regulated metabolic diversity. Microbiota plays an important role in flavor compounds formation during food fermentation. However, the role of initial microbial diversity in regulating flavor compounds formation is still unclear. Here, we used high-throughput amplicon sequencing and structural equation modeling to reveal the effect of initial microbial diversity on final metabolic diversity in Chinese sesame flavor-type liquor fermentation. The results showed that the initial fungal diversity positively impacted fungal succession (R = 0.74, P < 0.001). The longest fungal succession distance (0.054) was observed at the highest initial fungal diversity (38.580). Moreover, fungal succession positively affected metabolic succession (R = 0.71, P < 0.001), and the metabolic succession positively promoted the metabolic diversity (R = 0.68, P < 0.001). In addition, the longest succession distance of fungi (0.054) led to the longest succession distance of metabolites (0.065), and resulted in the highest metabolic diversity (0.409), that was significantly higher than the lowest metabolic diversity (0.219) (P < 0.05). Finally, a simulative fermentation experiment verified the significant and positive effect of initial fungal diversity on final metabolic diversity (R2 = 0.52, P < 0.05) in liquor fermentation. These results indicated the importance of initial fungal diversity for promoting flavor compounds formation. This work provides insights into improving flavor compounds formation by controlling initial fungal diversity in food fermentation, and it will be beneficial for improving the quality of fermented foods.