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Graphical abstract Highlights • The extraction solvent of six compounds was the tailored DES. • The extraction performance of DES is superior to that of traditional solvents. • The efficient and green DES-MAE extraction process was used in this study. • The extraction process of FSI was studied for the first time by kinetic experiments. • Target components were efficiently separated from DES. Abstract In the face of the many shortcomings of conventional organic solvents in the age of green chemistry, deep eutectic solvents (DESs) appear under the spotlight of natural product extraction because of its outstanding advantages. In this study, the extraction of six compounds from Flos Sophorae Immaturus (FSI) with DES-5 (choline chloride/1,4-butanediol) as its topgallant solvent was determined by screening nine DESs. After single factor test and BBD experiment, the optimum conditions of deep eutectic solvent-based microwave-assisted extraction (DES-MAE) were: choline chloride/1,4-butanediol (molar ratio of 1:2) and water content (25%, v/v), time 20 min, microwave power 600 W, temperature 62 ℃, liquid/solid ratio 26 mL/g. The extraction yields of rutin, nicotiflorin, narcissin, quercetin, kaempferol and isorhamnetin were 116.78, 15.01, 23.85, 27.59, 3.09 and 3.33 mg/g, respectively. The kinetic experiment results showed that DES-MAE has significant advantages in the extraction of six compounds. The experimental results showed that DES-MAE could obtain higher yields of target components in a short time than other methods (DES-HRE, DES-UAE and Ethanol-MAE). In addition, the target components were separated from the DES extraction solution, and the recoveries of the target compounds were in the range of 75.5%–84.1%. Therefore, this paper provides a strategy for extraction and separation, the aim of which is to obtain flavonoids from FSI efficiently. Meanwhile, this study can also be used as an alternative to the traditional methods for obtaining bioactive components from plant sources in biochemistry, food industry and pharmaceutical fields. [ABSTRACT FROM AUTHOR]