Geum japonicum Thunb. var. chinense (G. japonicum) is a cultivated medicinal plant and used as folk medicine, among which tannins are the main active ingredients. In this work, L-proline-lactic acid (Pro:La) as natural deep eutectic solvents (NADESs) was tailored for the total tannins extraction from G. japonicum with the optimal conditions as follows: water content of 29 %, solid-liquid ratio of 27:1 (mg/mL), extraction time of 48 min, and extraction temperature of 48°C. In high fat diet-induced obese mice, the total tannin extract of G. japonicum can significantly reduce the body weight and serum lipid levels, improve glucose tolerance impairment and insulin resistance, reduce islet hypertrophy and protect the liver. Targeted fractionation of the total tannin extract of G. japonicum led to the isolation of sixteen tannins. Notably, the isolated tannins, except for ellagic acid and 3,3′-di-O-methylellagic acid, possessed strong α-glucosidase inhibitory activities (IC50: 1.401–4.801 μg/mL) and dose-dependently inhibited glucose consumption of Caco-2 model system in vitro. These results indicate that the NADES (Pro:La) can effectively extract total tannins from G. japonicum and provide a reference for further applications in medicine and healthcare products.