[Background] Tripterygium is a traditional Chinese medicine with great value of clinical application for its diversity pharmacological activity. However, its lack of output and complicated extraction process limit the clinical application. Secondary metabolites of plant endophytic fungi can produce similar pharmacological activity, which is expected to solve the problem of lack of plant and become a potential resource for screening new drugs. [Objective] To isolate endophytic fungi from tripterygium wilfordii Hook.f., and screen their anti-microbial and anti-tumor activities in vitro. To transform the crude extracts of tripterygium wilfordii Hook.f. with active strains to achive increasing efficiency and reducing toxicity. [Methods] Endophytic fungi were isolated from tripterygium wilfordii Hook.f. with tissue block method; antibacterial activity against Staphylococcus aureus and Escherichia coli was tested with disk diffusion method; anti-tumor activity to two cell lines (MCF-7/SKOV3) was tested with MTT (Thiazolyl blue) assay. The ITS (Internal transcribed spacer) sequence sequencing analysis was used to identify the active strains species. [Results] 43 strains of endophytic fungi were isolated from Tripterygium wilfordii Hook.f. Five of them showed bacteriostasis to Staphylococcus aureus and the activity of LGT7 was similar to that of 1 μg/mL of penicillin sodium; 6 of them showed cytotoxicity to MCF-7 as well as SKOV3 and the growth inhibition ratio of LGT7 and LGT41 was above 90%; 4 of them showed transforming activity to crude extracts from Tripterygium wilfordii. The active strains were identified as Phomopsis sp. and Diaporthe sp.. [Conclusion] Endophytic fungi isolated from Tripterygium wilfordii Hook.f. have anti-microbial and anti-tumor activity in vitro. They can enhance the activity and reduce the toxicity by transformation.