Biochar is a promising carbon material to improve soil quality and relieve global warming by adding it into soil. Though biochar has been used for millennia as a soil ingredient, fundamental studies on the structure of biochar have only recently attracted great interest, and molecular-level structures are being pursued. In this study, by applying solvent exfoliation, high-resolution transmission electron microscopy with Cs-correction and quadrupole time-of-flight mass spectroscopy, we report, for the first time, an atomic-level observation of the fine aromatic cluster and molecular structure of the exfoliated biochars. The observed aromatic clusters are generally smaller than 5 nm and decorate the graphene-like aggregates at different depths. The Stone-Wales transformation in the dispersed biochars was observed, which is critical to form carbon nanotubes, fullerenes, and other carbon nanostructures in the natural environment. In addition, the C-C bond length decreases as the pyrolysis temperature increases from 500 to 700 °C, indicating that aliphatic carbon transforms into aromatic carbon. The quaternary structure of biochar, including heterogeneous phases, graphene-like aggregates, nanosized aromatic clusters, and atomic arrangements, is conceptualized to enhance our knowledge of the biochar structure, which greatly aids in understanding the novel functions of biochar and offers a molecular guide for potential applications of biochar.