Eucommia ulmoides Oliv. (E. ulmoides) is a kind of plant with high medicinal value, there are known as the "gold plants". Some components and contents of barks and branches from E. ulmoides are similar, the barks are mainly used as medicine, but the branches have not been systematically studied and were discarded. In this paper, five fractions extracted from E. ulmoides branches were detected by the classical anti-complement activity assay in vitro. The n-butanol fraction of E. ulmoides branches showed excellent anti-complement activities with a CH50 value of 0.016 ± 0.0014 mg·mL-1. A total of 76 compounds were identified from the n-butanol fraction, including 9 alkaloids, 18 organic acids, 22 lignans, 15 phenylethanoid glycosides and 12 other compounds. To further prove the anti-complement activity of potential active compounds, those compounds detectable in rat plasma after oral administration were tested by classical anti-complement activity assays. Genipin and pinoresinol 4-O-glucopyranoside had a certain complement inhibitory activity in the 17 potential anti-complements, their CH50 values were 0.050 ± 0.0038 and 0.022 ± 0.0018 mg·mL-1. UHPLC-Q-TOF/MS/MS was developed to profile and characterize the metabolites of genipin and pinoresinol 4-O-glucopyranoside in rat plasma. Twenty-one and seventeen metabolites were found, respectively. In summary, this study reported important clues for the further pharmacological and clinical studies of E. ulmoides branches. Meanwhile, it provided a practical strategy for rapid screening and identifying of in vivo anti-complement in traditional Chinese medicine.