Four compounds, Hypoxylonines A-D (1-4), were isolated from the ethyl acetate extract of the endophytic fungus Hypoxylon sp. derived from Cupressus funebris Endl., among them, Hypoxylonine A (1) is a previously unreported compound, although compounds 2-4, known from synthetic studies, are reported here for the first time as natural products. These compounds are structurally linked by a ketone carbonyl group to a toluene group and a cyclopentane unit. The structures of compounds 1-4 were elucidated by IR, HRESIMS, and one-dimensional and two-dimensional nuclear magnetic resonance (NMR) spectra. The NMR data of the new natural products (compounds 2-4) being reported for the first time. These compounds were evaluated for their inhibitory activities against phosphodiesterase 1 (PDE1) and Fusarium graminearum Schwabe. The results showed that compound 3 had strong inhibitory activity against PDE1 at a concentration of 100.0 μg/mL, with an inhibition rate of 78.70 ± 1.07% and an IC50 value of 40.78 ± 0.12 μg/mL.