We aimed to determine the content of peiminine in different tissues of F. hupehensis and species and secondary metabolites of its endophytes. Gas chromatography (GC) was used to determine the content of peiminine in bulbs, flowers and leaves of F. hupehensis. The 16S rDNA and ITS sequencing were used to identify the species of endophytic bacteria or fungi, respectively. And AGAR diffusion and double dilution method was used to study the antibacterial activity of secondary metabolites of endophytes against 10 strains of tested bacteria. The results were described below. Leaves of F. hupehensis had the highest content of peiminine with 3.99±0.10 mg?g-1, which was 1.78 and 4.24 times as much as bulb and flower respectively. Four strains of endophytes were isolated from F. hupehensis, identified as Pseudomonas sp. BM-X-6, Arthrinium sp. BM-Z-5, Aspergillus sp. BM-Z-1 and Aspergillus sp. BM-Z-3. The secondary metabolites of three endophytic fungi had stronger antibacterial activity than Pseudomonas sp.BM-X-6. Meanwhile Arthrinium sp. BM-Z-5 had the broadest antibacterial spectrum, which showed moderate antibacterial activities against Klebsiella pneumoniae, Staphylococcus aureus, Micrococcus luteus, Acinetobacter baumannii and methicillin-resistant Staphylococcus aureus(MRSA).