Flavonoid-rich leaves of the Ficus carica L. plant are usually discarded as waste. In this work, ultrasonic enzyme-assisted aqueous two-phase extraction (UEAATPE) was proposed as an innovative method to estimate the total flavonoids present in F. carica L. leaves. Total flavonoids were analyzed qualitatively and quantitatively by UPLC-QTOF-MS. At 38% (w/w) ethanol/18% (w/w) ammonium sulfate, we achieved the optimum conditions in which to establish an easy-to-form aqueous two-phase extraction (ATPE) as the final system. The optimal UEAATPE conditions were set at an enzymatic concentration of 0.4 U/g, 150 min enzymolysis time, an enzymolysis temperature of 50 °C, a liquid–solid ratio of 20:1 (mL/g), and 30 min ultrasonic time. The yields of the total flavonoids, i.e., 60.22 mg/g, obtained by UEAATPE were found to be 1.13-fold, 1.21-fold, 1.27-fold, and 2.43-fold higher than those obtained by enzyme-assisted ATPE (EAATPE), ultrasonic-assisted ATPE (UAATPE), ATPE, and soxhlet extraction (SE) methods, respectively. Furthermore, eleven flavonoids from the leaves of the F. carica L. plant were completely identified and fully characterized. Among them, ten flavonoids have been identified for the first time from the leaves of the F. carica L. plant. These flavonoids are quercetin 3-O-hexobioside-7-O-hexoside, 2-carboxyl-1,4-naphthohydroquinone-4-O-hexoside, luteolin 6-C-hexoside, 8-C-pentoside, kaempferol 6-C-hexoside-8-C-hexoside, quercetin 6-C-hexobioside, kaempferol 6-C-hexoside-8-C-hexoside, apigenin 2″-O-pentoside, apigenin 6-C-hexoside, quercetin 3-O-hexoside, and kaempferol 3-O-hexobioside. Therefore, F. carica L. leaves contain new kinds of unidentified natural flavonoids and are a rich source of biological activity. Therefore, this research has potential applications and great value in waste handling and utilization.