Gancao Ganjiang decoction (GGD) is one of the classic formulas in China known for its effective therapeutic effects in treating various diseases. Component research before and after the compatibility of Gancao and Ganjiang revealed that 6-gingerol content considerably changed. Compared with the decoction of Ganjiang, 6-gingerol in GGD demonstrated improved solubility. It was assumed that the partially hydrophilic glycyrrhizic acid and 6-gingerol self-assembled into nanoparticles, which then improved the solubility of 6-gingerol. The self-assembled nanoparticles in GGD were separated and characterized. Subsequently, 6-gingerol–glycyrrhizic acid nanoparticles (6-Gin-Gly NPs) were further prepared and characterized via dynamic light scattering (DLS) and transmission electron microscope (TEM). The formation mechanism of the self-assembled nanoparticles was examined using ultraviolet–visible spectroscopy (UV–vis), Fourier transform infrared spectroscopy (FTIR), electrospray ionization–mass spectrometry (ESI-MS), and molecular docking. The in vitro antioxidant activity of the 6-Gin-Gly NPs was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino bis(3-ethylbenzothiazoline-6- sulfonic acid)+ (ABTS+) free radical scavenging assays, which confirmed that the nanoparticles considerably enhanced their in vitro antioxidant capacity. In this study, the solubility of insoluble components was improved by the formation of self-assembled nanoparticles, which provided substantial reference data for the study of complicated multi-component interaction in herbal medicine decoction.