Natural deep eutectic solvents (DESs) were investigated as potential green extraction solvents in the ultrasound-assisted extraction (UAE) of flavonoids from Rubia truppeliana and R. cordifolia fruit. Lactic acid was selected as the optimal hydrogen bond donor for five solvents in the screening of DESs. To optimize the extraction of Rubia fruit flavonoids using DES and UAE, a Box–Behnken experimental design was developed. The optimal conditions were: liquid–solid ratio, 30; extraction temperature, 70 °C; and extraction time, 40 min. The corresponding yields were 49.41 mg/g for total flavonoids from Rubia truppeliana (TFT) and 55.15 mg/g for that of Rubia cordifolia (TFC). The extracts obtained under the optimum extraction conditions showed excellent antioxidant activities in DPPH, ABTS, and FRAP assays. The results demonstrated that the extraction using DES and UAE is an eco-friendly method for the extraction of flavonoids from Rubia fruit.