This study intends to explore the extraction mechanism of isoliquiritin by using experimental verification and molecular simulation techniques. Firstly, the Choline chloride (ChCl)-Citric acid (CA) deep eutectic solvent (DES) was prepared by the solvent method, and its structure was characterized by FT-IR, NMR, rheometer, molecular dynamics and quantum computation. The pharmacological activity and biosafety of DES were investigated by bacteriostasis and cell assay. The extraction mechanism of isoliquiritin by using synthesized ChCl-CA DES as extraction solvents were calculated by means of cohesive energy density (CED), mean square displacement (MSD) and radial distribution function (RDF). The results showed that compared with ethanol and water, DES as extraction solvent had the highest extraction yield of isoliquiritin. Through further study, it was found that the increase in the isoliquiritin extraction yield was mainly due to the strong molecular interaction between isoliquiritin and extraction solvent and the rapid diffusion of isoliquiritin.