Eurotium cristatum is the primary fungus in Fu brick tea (FBT) and plays a crucial role in its special flavor. This study investigated the effect of inoculation with different E. cristatum strains (i.e., ZJ, GX, GZ, HN, and SX) on the microbial communities and volatile organic compounds (VOCs) of FBT. A total of 113 VOCs were identified in all samples, with the concentration of VOCs (alcohols, aldehydes, and ketones) significantly higher in GXE FBT than in other samples. The core VOCs of GXE (19), GZE (16), HNE (19), SXE (15), and ZJE (13) FBT were identified using orthogonal partial least squares discriminant analysis and relative odor activity value (ROAV) analysis. Methional (a27), butanal (a41), 1-octen-3-one (a69), and ethyl acetate (a77) were key markers for inoculated FBTs, and 1-octen-3-ol, dimethyl disulfide, and acetoin-M were the specific markers of HNE. Linalool and (E)-2-octenal were particularly prominent in GXE, and isoamyl acetate-D was an important aroma component of GZE. Differences in microbial diversity were observed among the different inoculated fermented FBTs, and E. cristatum inoculation remarkably influenced the richness and diversity of bacterial communities. The VOCs were closely associated with fungi and bacteria, and 19 potentially dominant microorganisms (10 fungal and 9 bacterial genera) correlated with VOCs were identified. Among them, Aspergillus (fungi) and Pseudomonas (bacteria) exerted the greatest role. The FBT inoculated with E. cristatum from ZJ had the highest content of theaflavins and theabrownins, which intensified the red and yellow colors of the tea. E. cristatum greatly decreased the free amino acids and fatty acids, contributing to the aroma formation of FBT. Therefore, inoculating FBT with E. cristatum remarkably influenced the microbial communities and improved its flavor profile. This work provides a theoretical foundation on the role of E. cristatum in the formation and regulation of FBT flavor.