Berberine (BBR), isolated from Coptis chinensis, is one type of isoquinoline alkaloids. BBR exerts numerous of bioactivities but the plasma concentration is really low. In our previous study, a new oxymetabolite (OBB) has been discovered and showed superior anti-inflammatory effect comparing with BBR. The aim of this study is to investigate the interaction, metabolite and pharmacokinetics of BBR with hemoglobin. Sprague-Dawley rats were used to carry out the interaction, metabolite and pharmacokinetics of BBR and OBB in vivo. Fluorescence spectra were used to analyse the interaction in vitro. Results showed that OBB could be generated after intravenous injection or incubating with BBR in vitro and in vivo; Both BBR and OBB exerted much stronger binding interaction with hemoglobin than plasma and affect the conformation of bovine hemoglobin and change the fluorescence spectral properties; BBR and OBB were mainly presented and transported in the proteins-bound form. These results provide a new insight to understand the dynamic equilibrium of BBR and OBB within body from the perspective of new metabolic pathways.