Elucidating the underlying mechanism of the processing of Chinese herbal medicine (CHM) is crucial and also challenging for the modernization of Traditional Chinese Medicine (TCM). Herein, inspired by the traditional method for processing the Chinese herb Polygonum multiflorum (PM) Thunb with excipient black beans, the representative herbal components trans-2,3,5,4'-tetrahydroxystilbene 2-O-β-D-glucopyranoside (TSG) and cyanidin-3-O-β-glucoside (C3G) from each herbal medicine were selected to investigate the processing mechanism at the supramolecular level. The co-assemblies of TSG/C3G were found to be formed, and their structure was characterized by electronic microscopy and a small angle X-ray scattering (SAXS) technique. In addition, the supramolecular interactions between TSG and C3G were fully probed with UV-Vis, fluorescence, XRD, and NMR spectroscopy. Molecular dynamics were further performed to simulate the assembly processes of TSG and C3G. Notably, the formation of TSG/C3G co-assemblies was found to significantly enhance the stability of TSG against light, Fe3+, and simulated intestinal fluids. The co-assembly of TSG and C3G that leads to supramolecular aggregates discovered here may imply the underlying mechanism of processing PM with black beans. Our results may also suggest that a new effective form of TCM is supramolecular aggregates rather than each component.