Marine fungal natural products are valuable sources of structurally diverse and biologically active compounds with potential applications in drug discovery and biotechnology. The fungus Penicillium crustosum is an important source of bioactive natural products that display significant antibacterial properties. This study describes the isolation and characterization of two new structures including one γ-unsaturated lactone named crustosulin A and one aliphatic acid named crustosenoic acid A along with ten known compounds from a marine-derived fungus Penicillium crustosum HDN17-68, which is isolated from the Western Pacific deep-sea mud sample. Compounds were isolated and purified through column chromatography and HPLC, and structures were elucidated using spectroscopic tools including NMR, MS, and ECD. Compound 1 represents the first example of a dimeric γ-unsaturated butyrolactone incorporating a β-to-α connectivity and it exhibited weak activity against Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA), with MIC values of 32 and 64 µg/mL, respectively. These findings expand the chemical diversity of secondary metabolites from deep-sea-derived Penicillium fungi.