Doubanjiang is a special Chinese seasoning paste produced by mixing broad bean paste with chili paste. Besides the antimicrobial substances, such as capsaicin contained in chili, the microbiota and metabolism are directly developed by the stress effect of abiotic factors that periodically change during the fermentation process. The microbial starter is a promising way to improve the quality of Doubanjiang production. In the present study, the regulatory mechanisms of the microbial starters (Tetragenococcus halophilus, Zygosaccharomyces rouxii, and Candida versatilis) were explored by comparing the microbial community, flavor characteristics and their correlation networks between the fortified and control groups. In comparison to the control group, the volatile compound content increased by 30.77%, with notable increases in phenylethyl alcohol, beta-ionone, etc. Conversely, there was a reduction in non-volatile compounds, including reducing sugar, acidity, amino acid nitrogen, and organic acids. The microbial structure underwent a shift, with an increase in the relative abundance of C. versatilis, while Z. rouxii demonstrated no variance and T. halophilus was not detected. The correlations of the specific microbes and certain flavor compounds were modified by the starter (p < 0.05). Notably, the correlation between Enterobacter/Malassezia and 3-furaldehyde was shifted from a negative to a positive conversion. The observed increase in beta-ionone, ethyl phenylacetate, etc., resulted from the synergistic effects, correlated transformations, and reduction of antagonistic interactions. These findings indicate that the starter powerfully regulates the interactions between microbial communities and metabolic networks, thereby provide valuable insights for the improvement of Doubanjiang quality.