Microcos paniculata L. (ML) is an edible herbal tea plant with regional differences in flavor and bioactive quality. However, the chemical and microbial factors associated with these differences remain unclear. This study integrated HS-GC-Orbitrap-MS/MS, 16S rRNA sequencing, sensory evaluation, color analysis, and antioxidant assays to characterize ML samples from Guangdong, Guangxi, and Yunnan, China. Guangdong samples were characterized by the highest total phenolic and flavonoid contents and superior antioxidant capacity, whereas Yunnan samples showed the best sensory performance, particularly for aroma and taste attributes. A total of 133 volatile constituents were tentatively identified, mainly comprising olefins and cycloolefins, aromatic compounds, terpenes, alcohols, and ketones. Chemometric analysis revealed clear origin-dependent separation and identified 12 differential volatile compounds, including p-cymene, L-limonene, α-phellandrene, dimethyl sulfide, and ethylbenzene. Bacterial community analysis showed distinct origin-associated patterns, and several bacterial taxa were correlated with characteristic volatile compounds and quality traits. Functional prediction and multivariate correlation analysis suggested potential associations among environmental factors, bacterial communities, volatile metabolites, and antioxidant properties. These findings provide a foodomics-based framework for understanding geographical quality variation in ML and offer potential markers for origin traceability and quality evaluation of edible herbal tea resources.