This study employed deep eutectic solvents (DES) combined with ultrasonic-assisted extraction technology to green and efficiently extract flavonoids from honeysuckle, and systematically evaluated its inhibitory mechanism on α-amylase (α-AMY). Through comparative screening of six DES systems and traditional solvents, DES-4 (Choline chloride–propylene glycol) was identified as the optimal extraction solvent. After single-factor and response surface optimization, the yield of honeysuckle flavonoids (HF) was significantly increased to 9.12 ± 0.08% under the conditions of ultrasonic power 300 W, solid–liquid ratio 1:32 (g/mL), and extraction time 60 min. HPLC-MS analysis revealed that luteolin (4.59 ± 0.09 mg/g) and quercetin (3.05 ± 0.02 mg/g) were the main active components, and they exhibited strong antioxidant activity. Enzyme kinetics and Lineweaver–Burk analysis indicated that the inhibition type of HF on α-AMY was reversible mixed inhibition. Fluorescence spectroscopy, thermodynamic analysis, and molecular docking results further revealed that HF primarily bound to α-AMY through hydrogen bonds and van der Waals forces (ΔH = −63.80 kJ/mol, ΔS = −0.19 J/mol·K), causing static fluorescence quenching and altering its hydrophobic microenvironment and spatial conformation. This study aims to provide new theoretical basis for the green and efficient extraction of HF and its development and application in functional foods and natural medicines.