Natural bioactive compounds extracted from agricultural by-products have received considerable attentions. Twenty-two kinds of deep eutectic solvents (DESs) with ultrasonic were screened to extract flavonoids from peanut leave and stem. ChCl-acetic acid (ChCl-Aa) with 1:2 M ratio resulted in more effective extraction of flavonoids compared to other solvents The best extraction conditions were found to be at a 27% water content in DES/H2O, for 43 min with 31:1 g/mL liquid/solid ratio, giving 2.980 mg/g dw of flavonoids through the response surface method. SEM showed that ChCl-Aa had a certain dissociation impact on the sample matrix, while 1H NMR analysis revealed the formation of hydrogen bonds between daidzein and ChCl-Aa. Changes in the H-bond length and number were observed by the B3LYP/6-31G (d,p) level of theory to confirm the experimental spectra. This study reveals that DESs are efficient for obtaining value-added products and could applied to other natural products.