Lipase is a very important digestive enzyme for triglyceride absorption in vivo. The inhibitory activities of 26 dietary flavonoids, including flavone, flavanone, isoflavone and flavanol, on lipase were determined. Flavone exhibited stronger inhibitory activity than other types of flavonoids. Among them, luteolin exhibited the strongest inhibitory activity with IC50 value of 99 ± 11 μM, followed by quercetin and baicalein. The binding affinity of these flavonoids with lipase was investigated by fluorescence titration method. The binding affinity of flavones was stronger than flavanones, and was linearly positively correlated with their inhibitory activity. The binding of flavones on lipase caused the blue-shift of fluorescence, while flavanones caused red-shift. The analysis of structure-activity relationship of flavonoids on lipase revealed that the structure of C ring is very crucial. The hydrogenation of C2=C3 bond and the absence of C=O group in C ring both caused significant decrease of inhibitory activity. Besides, the hydroxylation on ring A and B of flavones increased the activity, while glycosylation weakened the activity. Molecular docking analysis confirmed that C2=C3 bond in C ring of flavones increases the π-conjugation and contributes to maintaining the planarity of flavonoid structure, which favour its Pi-Pi interaction with lipase.