Inflammation is a common and important pathological process, and nuclear factor-κB (NF-κB) is a key mediator of it. Moutan Cortex (MC), the dried root cortex of Paeonia suffruticosa Andr., is widely used as a remedy for the treatment of inflammatory diseases in Asian region. However, there are few studies on the systematic identification of NF-κB inhibitors of MC. In this study, the effect of inhibiting NF-κB activation of MC was assessed at the cellular level using a tumor necrosis factor-α (TNF-α) induced inflammatory model. Subsequently, ultra-performance liquid chromatography-quadrupole/time of flight-mass spectrometry (UPLC-Q/TOF-MS) combined with biological activity assay was established to screen and identify potential anti-inflammatory ingredients in MC. The results revealed that MC significantly inhibited the activation of NF-κB. Seven potential NF-κB inhibitors were screened from MC, including oxypaeoniflorin, paeoniflorin, galloylpaeoniflorin, benzoyloxypaeoniflorin, mudanpioside C, gallic acid, and paeonol. Among them, the NF-κB inhibitor activity of galloylpaeoniflorin, benzoyloxypaeoniflorin, and mudanpioside C is first reported here. In conclusion, the anti-inflammatory activity of MC was associated with the seven components mentioned above. And the bioactivity-integrated UPLC-Q/TOF which contains both chemical and bioactive details is suitable for screening active ingredients from natural medicines.