As the number of viruses, bacteria, and tumors that are resistant to drugs continues to rise, there is a growing need for novel lead compounds to treat them. Marine fungi, due to their unique secondary metabolic pathways and vast biodiversity, have become a crucial source for lead compounds in drug development. This review utilizes bibliometric methods to analyze the research status of natural products from marine fungi in the past decade, revealing the hotspots and trends in this field from Web of Science database. Furthermore, this review summarizes the biological activities and effects on molecular mechanisms of novel natural compounds isolated from marine fungi in the past five years. These novel compounds belong to six different structural classes, such as alkaloids, terpenoids, anthraquinones, polyketones, etc. They also exhibited highly potent biological properties, including antiviral, antitumor, antibacterial, antiinflammatory, and other properties. This review demonstrates the hotspots and trends of marine fungi research in recent years, as well as the variety of chemical structure and biological activities of their natural products, and it may provide guidance for those interested in discovering new drugs from marine fungi and specific targeting mechanisms.