Hinokiflavone (HF), belonging to biflavonoids, possesses excellent pharmacological activities, including anti-inflammatory, antioxidant and antitumor activity. Nevertheless, its metabolism in vivo (rats) and in vitro (rat liver microsomes and intestinal flora) is presently not characterized. In this study, ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) based on four-step strategy was a rapid method for the detection of HF metabolites. A total of 41 metabolites in vivo, 49 metabolites in vitro were characterized. It also verified that intestinal tract exceeds the liver in the biotransformation of HF. More significant, the main metabolic pathways for HF were mainly bio-transformed to various mono-flavone resulting from the rupture of connective CO bonds, which exhibited a large distinction with other biflavones. Noteworthily, glutamine conjugation and glycine conjugation were considered as unique metabolic pathways of HF. The information obtained from this study contributes to better understanding of pharmacological mechanism of HF.