The ethyl acetate fractions prepared from the leaves of Thuja orientalis significantly inhibited nitric oxide (NO) production in lipopolysaccharide-stimulated BV2 microglial cells. According to bioassay-coupled LC-QTOF MS/MS, the components near 22 and 25 mins in the mass chromatogram highly inhibited NO production and were expected to be labdane diterpenes, and the active components were characterized via further isolation. The results of the NO production inhibitory assay of the isolated compounds correlated well with the results of bioassay-coupled LC-QTOF MS/MS. Among the identified constituents, NO production inhibitory activities of 16-hydroxy-labda-8(17),13-diene-15,19-dioic acid butenolide (2) and 15-hydroxypinusolidic acid (3) were newly reported. Taken together, these results demonstrated that LC-QTOF MS/MS coupled with NO production inhibition assay was a powerful tool for accurately predicting new anti-inflammatory constituents in the extracts from natural products. Moreover, it provided a potential basis for broadening the application of bioassay-coupled LC-QTOF MS/MS in natural product research.