Flavones are an important class of bioactive constituents in foods, and their structural diversity enables them to interact with different targets. In particular, flavones are known for their anti-inflammatory activity. Herein, we summarized commonly applied in vitro, in vivo, and clinical models in testing anti-inflammatory activity of flavones. The anti-inflammatory structure−activity relationship of flavones was systematically mapped and supported with cross comparisons of that with flavanones, flavanols, and isoflavones. Hydroxyl groups (−OH) are indispensable for the anti-inflammatory function of flavones, and −OH at the C-5 and C-4′ positions enhance while −OH at the C-6, C-7, C-8, and C-3′ positions attenuate their activity. Moreover, the C2−C3 single bond, −OH at the C-3 and B-ring positions undermine flavone aglycones' activity. Most of the flavone aglycones function through NF-κB, MAPK, and JNK-STAT pathways, and their possible cell binding targets are kinase, aryl hydrocarbon receptor (AhR), G-protein coupled receptors, and estrogen receptors. However, the structure and anti-inflammatory activity relationship of flavones were unclear, and further research shall be conducted to close the gap in order to guide development of evidence-based functional foods.