Two new xanthone compounds, austocystin S (1) and austocystin R (2), as well as three known xanthones (3-5), originated from endophytic Aspergillus puniceus strains isolated from Eupatorium chinense tissues. Structural elucidation of the compounds was achieved by employing spectroscopic methods such as NMR, MS, CD, and X-ray diffraction. Each of the five compounds exhibited inhibitory effects on Protein Tyrosine Phosphatase 1B (PTP1B). Both compound 1 (IC50 = 2.89 μM) and compound 2 (IC50 = 0.78 μM) displayed notable inhibition effects. The inhibitory profiles of compounds 2 and 3 varied among the nine tested tumour cell lines, though both showed preferential activity against MDA-MB-231 cells (1.45 μM and 1.28 μM IC50 values, respectively). Molecular docking studies were performed to assess the binding interactions of compounds 1 and 2 with PTP1B.The calculated results showed that both compounds 1 and 2 had strong binding affinity for PTP1B.