Smilax glabra Roxb. (SG) is widely used as functional food with various beneficial effects. Fresh SG without processing has been eaten directly for anti-inflammation from ancient China, while the underlying mechanism remains underexplored. This study aims to investigate the anti-inflammatory activity of fresh SG by using metabolites profiles, affinity ultrafiltration mass spectrometry, PDE4 enzyme inhibition assay, and in silico analysis. Encouragingly, fresh SG showed promising anti-inflammatory effect with IC50 value (0.009μg/μL) on PDE4 was about 12 times higher than that of processed SG (0.110μg/μL). Astilbin was identified as the main bioactive compound of fresh SG responsible for PDE4 inhibitory activity. We found that heat processing strongly affected astilbin isomerization, leading to significant changes in contents and PDE4 inhibitory activities of four astilbin isomers, resulting in decreased anti-inflammatory activity of fresh SG. This finding will provide theoretical basis for systematic research and food/nutraceutical applications of fresh Smilax glabra in the future.