Fulvic acid (FA) is important in modern agriculture, ecological restoration, life science, and medicine. The precise characterization of the composition and molecular structure of FA has become a key scientific issue in both basic and applied research. In this study, coal-based FA was separated by microwave-assisted oxygenation from lignite originating from Inner Mongolia in China. Through elemental analysis, infrared spectroscopy, nuclear magnetic resonance spectroscopy, classical quantitative titration experiments, and quantum chemistry combined with software analysis, the representative microscopic molecular structure of FA was determined. The results show that coal-based FA mainly contains three kinds of benzene ring substituents, ether bonds, hydrogen bonds, carbonyl groups, hydroxyl groups, carboxyl groups, phenolic hydroxyl groups, and semiquinonyl groups. The oxygen content is high, the carbon-to-oxygen ratio is less than 1, and the hydrogen-to-carbon ratio is 1.09. The ratio of aromatic carbon to total carbon is approximately 0.6, and benzene rings are connected to each other by an ether–oxygen bridge. The fat chain length of FA is approximately 0.47. FA has a small molecular structure with many acidic groups, primarily carboxyl groups and phenolic hydroxyl groups. The two-dimensional planar molecular structure of FA was established; the chemical formula is C₃₈H₃₂NO₂₄, and the relative molecular mass is 886. The lowest-energy, structurally optimized three-dimensional characteristic ball-and-stick and stick models were also constructed. The calculated infrared spectrum of the molecular structure matches well with the experimental spectrum of FA, and the types and distributions of functional groups agree with the findings of previous studies. The quantum chemical data confirm that the proposed molecular structure is reasonable. The findings provide a scientific reference for applied research on FA in the future.