A new radio frequency heating-assisted enzymatic extraction (RF-E) method is applied for the determination of phenolic compounds in Akebia trifoliata flowers, compared with hot water, acidified ethanol (EtOH), and enzymatic-assisted (EA) extractions. Non-anthocyanin polyphenol profiles, antibacterial, angiotensin-converting enzyme (ACE) inhibitory, anti-inflammatory activities, and structures of extracts are evaluated. Results show no significant differences in the extraction of total flavonoid content (15.85-16.63 mg QEs/g) and ACE inhibitory activity (51.30-52.86%) between RF-E and EA extracts. RF-E extract shows the highest anti-inflammatory activities. FTIR and UV spectra reveal that acidified EtOH treatment has a significant effect on the structure of the extract due to its highest flavonoid content (20.33 mg QEs/g), thus it has the highest antibacterial activity against Staphylococcus aureus and Escherichia coli. Sixteen non-anthocyanin polyphenols are identified by UPLC-PDA-TOF-ESI-MS and RF pre-treatment did not cause significant compound degradation. The chemometric analysis shows that enzymatic hydrolysis significantly increased biological activities, and the presence of non-anthocyanin polyphenols correlates well with ACE inhibitory and anti-inflammatory activities. Accordingly, A trifoliata flowers have potential as reagents for the food and pharmaceutical industries due to their abundant polyphenols that could be extracted efficiently using RF-E.