Abstract: In order to study the contraindications of the compatibility of Flos Genkwa-Radix et Rhizoma Glycyrrhizae, in this study, the solubilizing and poisoning essence were explored. In this experiment, chromatographic assay, field emission scanning electron microscopy, MTT cytotoxicity evaluation, and other methods were used to study the main chemical components, morphology and toxicity of the ethyl acetate part of Flos Genkwa and its co-decoction with glycyrrhizic acid, in order to clarify Flos Genkwa-Radix et Rhizoma Glycyrrhizae incompatibility provides a new idea for the research on incompatibility of Flos Genkwa-Radix et Rhizoma Glycyrrhizae. The results showed that after co-decoction of the ethyl acetate part of Flos Genkwa with glycyrrhizic acid, high performance liquid chromatography (HPLC) detected the dissolution of the toxic component yuanhuacine of 54.8%, while yuanhuacine chromatographic peak was not detected in the Flos Genkwa ethyl acetate part of the single decoction. The increase of co-decoction dissolution rate was observed by scanning electron microscopy, and it was found that glycyrrhizic acid uniformly dispersed the fat-soluble components of Flos Genkwa into nano-scale particles, which improved the solubility and stability in the solution. Furthermore, the results of cytotoxicity evaluation showed that the survival rate of cells decreased after co-decoction, 4',6-diamidino-2-phenylindole (DAPI) staining also gave the same results. In summary, the co-decoction of the ethyl acetate part of Flos Genkwa with glycyrrhizic acid promotes the dissolution of the toxic component yuanhuacine, and makes the part form uniformly distributed nanoparticles, which is conducive to the absorption of the ingredient and increases the toxicity.