Abstract: Humic acid is a natural or synthetically produced macromolecular material. Due to its diverse functions—such as promoting efficient nutrient utilization, stimulating crop growth, enhancing crop stress resistance, improving soil structure, and mitigating heavy metal contamination in soil—it plays a significant role in enhancing green efficiency in agriculture. Existing commercial humic acids are mainly sourced from natural materials such as lignite and weathered coal, as well as from artificial humic acids produced through biological processes using agricultural residues, including crop straw and livestock or poultry manure. Their complex chemical structures and variable agronomic functions severely limit their precise and efficient utilization. The agronomic efficacy of humic acid is closely related to its structure, making structure-based functional modification a core challenge and a hotspot topic at the forefront of current research on humic acid. Therefore, this article systematically reviews research progress in the sources, structural and characteristic differences of humic acid, biological, chemical, and physical modification methods and mechanisms for regulating the functions of natural humic acid, functional modification methods and mechanisms for artificial humic acid, underlying mechanisms of humic acid in enhancing agricultural efficiency, along with key functions and structural features. Humic acid from different sources exhibits high heterogeneity in structure and properties, with significant variations in chemical composition, aromaticity, molecular weight, functional groups, and spectral characteristics. Natural humic acid can be modified via in situ or ex situ biological, chemical, or physical methods, and artificial humic acid can be modified through in situ synthesis. These modifications primarily target structural parameters, including elemental ratios, molecular weight, and functional groups. The underlying mechanisms and key structural determinants of humic acid effects vary across different applications for enhancing agricultural green efficiency, primarily relating to its molecular weight, aromaticity, and functional groups. Future research should further deepen the mechanistic understanding of humic acid functions in agricultural systems, identify its key functional structures, and precisely establish quantitative relationships between the enhancement of agricultural green efficiency and the functional structures of humic acid, thereby providing a scientific basis for the functional regulation and quantitative application of humic acid. Research should also be strengthened on the isolation and identification of microbial strains capable of promoting the targeted humification of straw, livestock and poultry manure, and other organic substrates, thereby enhancing the functions of biologically modified humic acids or humification-derived products. In addition, efforts should be intensified to investigate physicochemical technologies for the functional grading and directional regulation of humic acids, to supply high-quality humic acid products through refined functional modulation. In summary, improving the functional performance of humic acid products through regulatory methods and mechanistic studies will provide efficient and high-value products that synergistically promote green agricultural development and safeguard food security.