Caper (Capparis spinosa L.) fruits have been widely used as food and folk medicine in the Mediterranean basin and in central and west Asia. In this study, two biflavonoids, isoginkgetin, and ginkgetin, together with three other flavonoids, were isolated from caper fruits. Their chemical structures were elucidated by spectroscopic analyses and comparison with literature. To our knowledge, isoginkgetin, ginkgetin and sakuranetin were identified in caper for the first time. Notably, it is also the first time that biflavonoids have ever been found in the Capparidaceae. Concentrations of the two biflavonoids were measured in caper fruits collected from four major growing areas in northwest China. The anti-inflammatory effects of the flavonoids from caper fruits were evaluated by secreted placental alkaline phosphatase (SEAP) reporter assay, which was designed to measure nuclear factor-kappa B (NF-κB) activation. Isoginkgetin and ginkgetin showed inhibitory effects in initial screen at 20 μM, while the effect of ginkgetin was much greater than that of isoginkgetin. In a dose-response experiment, the IC(50) value of ginkgetin was estimated at 7.5 μM, suggesting it could be a strong NF-κB inhibitor and worthy of study in vivo.