The scarcity of agarwood resources has become a key bottleneck limiting its industrial application, and agarwood leaves—a major byproduct of agarwood cultivation—urgently require high-value development. To investigate the effects of microbial fermentation on the functional components and metabolic regulation of agarwood leaf essential oil, this study used agarwood leaves as raw material and inoculated them with Penicillium camponotum and Phaeoacremonium scolyti, respectively, for solid-state fermentation. Essential oil was obtained via subcritical extraction, and the changes in the composition of non-volatile metabolites in the agarwood leaf essential oil before and after fermentation were systematically analyzed using UHPLC-MS/MS-based broad-range targeted metabolomics. The results showed that 981 metabolites were identified in the agarwood leaf essential oil. PCA and OPLS-DA analyses revealed significant differences in the metabolic profiles among the three sample groups, indicating that both fungi effectively reshaped the metabolic network of the agarwood leaf essential oil. The relative proportion of flavonoid metabolites increased from 39.43 wt.% in the unfermented sample to 55.51 wt.% in the CXYPC sample and 74.08 wt.% in the CXYPS sample. KEGG pathway enrichment analysis revealed a significant enrichment of differentially expressed metabolites in pathways such as flavonoid biosynthesis and phenylpropanoid biosynthesis. Differences in specific regulatory patterns between the two strains: Penicillium camponotum tended to promote the accumulation of structurally modified flavonoid products, whereas Phaeoacremonium scolyti primarily maintained the enrichment of glycosylated flavonoids. This study provides a theoretical basis for the high-value utilization of agarwood leaf by-products, as well as feasible strategies and scientific support for enhancing the levels of bioactive components in agarwood leaves through directed fermentation and for screening superior fermentation strains.