The genus Daldinia have long been recognized as a source of structural novel, pharmaceutically relevant natural products. We reviewed the structures and activities of secondary metabolites isolated from the genus of Daldinia from January 1995 to June 2024, and 280 compounds, including six major categories—terpenoids, alkaloids, polyketides, polyphenols, steroids, and other classes—are presented in this review. Among these metabolites, 196 were identified as new structures. Remarkably, 112 compounds exhibited a range of biological activities, including cytotoxic, antimicrobial, anti-inflammatory, antifungal, anti-virus, and enzyme-inhibitory activities. This review highlights the bioactive metabolites discovered in the past three decades from the genus of Daldinia while also exploring the potential of these symbiotic fungi as rich sources of novel and diverse natural products. The varying bioactivities of these metabolites offer a vast array of promising lead compounds and also could significantly contribute to the development of new medicines.