Background: Phillyrin and (+)-pinoresinol 4-O-β-D-glucoside are the major active furofuran-type lignans in Fructus Forsythiae. The metabolic routes and metabolites of these two lignans are not well understood yet. Objective: In this study, we attempted to identify the human-intestine bacterial metabolites of lignans from Fructus Forsythiae. Materials and Methods: Two natural compounds, phillyrin and (+)-pinoresinol 4-O-β-D-glucoside were incubated with human fecal microflora in an anaerobic incubator for 72 h and the metabolites with highly sensitive ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) were analyzed. Results: As a result, nine metabolites were determined using a Syncronis™ C18column (particle size 1.7 mm) in a gradient elution system. These metabolites were then identified according to the mass fragmental mechanism, MS/MS fragment ions, and previous publications. The results of this study indicated that the major metabolites of furofuran-type lignans are through the processes of hydrolysis, demethylation, reduction, dehydroxylation, and oxidation. Conclusions: Lignans can be metabolized by intestinal microbiota and the intestinal bacteria play a critical role in the metabolism of components administered orally. Abbreviations used: GAM: General anaerobic medium; UPLC/Q-TOF-MS: Ultra-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry; ESI: Negative ion electrospray; RT: Retention time; TCM: Traditional Chinese Medicine.