The purpose of the present study was to discover antimicrobial endophytic fungi from <i>Astragalus chinensis.</i> Three fungal endophytes with antibacterial activity were isolated and determined as <i>Chaetomium</i> sp. HQ-1, <i>Fusarium</i> sp. HQ-7 and <i>Fusarium</i> sp. HQ-9 based on the neighbor-joining phylogenetic tree. <i>Chaetomium</i> sp. HQ-1 showed the best antibiotic potential and was thus selected for large-scale fermentation. Bioactivity-directed separation of ME fermentation of strain HQ-1 led to the discovery of three compounds, which were identified as differanisole A (<b>1</b>), 2,6-dichloro-4-propylphenol (<b>2</b>) and 4,5-dimethylresorcinol (<b>3</b>), from the HR-ESI-MS and NMR data analysis. All three compounds exhibited moderate antibacterial activity against <i>Listeria monocytogenes</i>, <i>Staphylococcus aureus</i>, and methicillin-resistant <i>S. aureus</i>, with MIC values ranging from 16 to 128 μg/mL. Compounds <b>1</b> and <b>3</b> also displayed promising antifungal activity against <i>Selerotium rolfsii</i> with IC₅₀ values of less than 16 and 32 μg/mL, respectively, which were comparable to that of actidione (8 μg/mL). The findings of the present study suggest that the endophytic fungi from <i>A. chinensis</i> have the potential to be used as bactericides and fungicides.