Phillyrin is a critical bioactive constituent of Forsythiae Fructus, exhibiting multiple pharmacological properties, but suffers from poor membrane permeability and low oral bioavailability. In this study, we developed a novel, green method employing whole-cell biocatalysts and natural deep eutectic solvents (NADESs) for the cinnamoylation of phillyrin to improve its liposolubility and bioactivity. Aspergillus oryzae whole cells showed high catalytic activity and stability in co-solvent systems containing hydrophobic NADESs. The NADES-tetrahydrofuran (50%, v/v) mixture maintained a high conversion rate (97.32–99.00%) and excellent 6′-regioselectivity (>99%) under optimal conditions (20 mg·mL−1 whole-cell dosage, 15:1 vinyl cinnamate/phillyrin, at 50 °C). Crucially, Aspergillus oryzae whole-cell biocatalysts exhibited markedly enhanced operational stability across all tested NADES-tetrahydrofuran (50%, v/v) reaction systems, retaining 80.09–97.95% of their original activity after six consecutive batch cycles. This study successfully combined hydrophobic NADESs with a whole-cell biocatalytic system, achieving efficient and regioselective cinnamoylation of phillyrin.