Two new nucleoside derivatives, kipukasins O (1) and P (2), one new cyclohexenone derivative, arthropsadiol D (5), and one new natural product, (+)-2,5-dimethyl-3(2H)-benzofuranone (6), together with eleven known compounds (3, 4, 7-15), were obtained from the culture broth of the endophytic fungus Aspergillus polyporicola R2 isolated from the roots of Synsepalum dulcificum. Among them, the absolute configuration of compound 5 was determined by quantum chemical calculations of NMR chemical shifts and ECD spectrum. The antimicrobial activities of these compounds were evaluated. Compound 11 exhibited obvious inhibitory activity against MRSA, Staphylococcus aureus, Salmonella typhimurium, Botrytis cinerea, and Fusarium graminearum with MIC values of 4, 4, 4, 32, and 16 μg/mL, respectively. Compound 12 exhibited antibacterial activity against S. typhimurium and MRSA with MIC values of 4 and 16 μg/mL. Compound 6 exhibited antifungal activity against F. graminearum with MIC value of 32 μg/mL.