Dehydrodiisoeugenol (DDIE), a representative and major benzofuran-type neolignan in Myristica fragrans Houtt., shows anti-inflammatory and anti-bacterial actions. In order to better understand its pharmacological properties, xenobiotic metabolomics was used to determine the metabolic map of DDIE and its influence on endogenous metabolites. Total thirteen metabolites of DDIE were identified through in vivo and in vitro metabolism, and seven of them were reported for the first time in the present study. The identity of DDIE metabolites was achieved by comparison of the MS/MS fragmentation pattern with DDIE using ultra-performance chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI- QTOFMS). Demethylation and ring-opening reaction were the major metabolic pathways for in vivo metabolism of DDIE. Recombinant cytochrome P450 s (CYPs) screening revealed that CYP1A1 is a primary enzyme contributing to the formation of metabolites D1-D4. More importantly, the levels of two endogenous metabolites 2,8-dihydroxyquinoline and its glucuronide were significantly elevated in mouse urine after DDIE exposure, which explains in part its modulatory effects on gut microbiota. Taken together, these data contribute to the understanding of the disposition and pharmacological activities of DDIE in vivo.