In order to investigate the chemical components of ethyl acetate extracts from the deep-sea fungus Penicillium sp. SZWQM-1, compounds were isolated and purified using various column chromatography techniques, and their structures were identified by NMR, MS, and IR methods. The in vitro antioxidant activity of the isolated compounds 1-7 was assessed using the DPPH scavenging methods. Seven compounds were isolated from the EtOAc extract of Penicillium sp. SZWQM-1, including penithol (1), penithochromone U (2), penithochromone R (3), penithochromone A (4), penithochromone P (5), penithochromone J (6), penithochromone K (7), of which compounds 1 and 2 were new compounds, named penithol and penithochromone U, respectively. The results of the activity experiment showed that compounds 1 and 3 had DPPH free radical scavenging rates of 55.9% and 40.9% at a concentration of 1 mmol/L, indicating that compounds 1 and 3 have moderate scavenging abilities against DPPH free radicals.