Two new polyketides with a 6/6/6 oxygenated heterocyclic ring system, eupenicillmarines A–B (1–2), one new alkaloid eupenicillmarine C (3), one new natural product alkaloid eupenicillmarine D (4), and four known compounds (5–8), were isolated from the marine-derived fungus Eupenicillium sp. HJ002. Their structures and absolute configurations were elucidated by 1D/2D NMR, HR-ESI-MS spectral, ECD calculation, and X-ray diffraction analyses. Eupenicillmarine A (EMA) exhibited potent nematicidal activity against Meloidogyne incognita with an EC50 of 32.7 μg/mL. EMA effectively inhibited the M. incognita egg hatching and caused significant morphological distortions. EMA induced oxidative stress imbalance by decreasing antioxidant enzyme activity, leading to excessive ROS accumulation, which reduced soluble protein levels and ATP levels and disrupted energy metabolism. EMA exhibited a significant treatment effect against M. incognita in chili pepper plant experiments and remaining safe for rice crops, suggesting its potential as a promising, environmentally friendly nematode control agent.