The green deep eutectic solvents(DESs) synthesized by choline chloride(ChCl) were applied to extract the total flavonoids, total quercetin and quercetin from Chrysanthemum indicum L.. Firstly, four kinds of DESs with excellent performance were synthesized and their physical properties were characterized. Secondly, urea-choline chloride with the best extraction effect was used as the solvent to optimize several parameters affecting the extraction amount. The extraction conditions were as follows: water content of 30%, extraction time of 45 min, solid-liquid ratio of 1:50 g/mL, extraction temperature of 60 ℃. At this time, the extraction yields of total flavonoids, total quercetin and quercetin were 72.32 mg/g, 12.97 mg/g and 10.06 mg/g, respectively, which were better than traditional organic solvents. Finally, the SEM and XRD results showed that the crystal structure of the Chrysanthemum indicum L. did not change significantly during the extraction process. DESs can dissolve the lignin on the surface of Chrysanthemum indicum L., which makes it have stronger cell-breaking effect and leads to easier dissolution of flavonoids.