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Endophytes are symbiotic microbial communities residing within plants and represent a significant source of bioactive secondary metabolites. As integral components of plant microecosystems, endophytes establish stable and mutually beneficial interactions with their hosts, which not only contribute to plant growth and stress resistance but also drive the diversity of their secondary metabolic products through long-term coevolution. These metabolites exhibit diverse biological activities, including anti-inflammatory, antimicrobial, cytotoxic, antiviral, and antioxidant effects, and these bioactive properties make them promising candidates for the development of new agents in multiple fields, including pharmaceuticals, agrochemicals, and functional materials, due to their natural origins and relatively low environmental impact. This review comprehensively summarizes recent advances in understanding the bioactivities of endophyte-derived secondary metabolites, highlighting novel compounds and their pharmacological potential. Alongside traditional approaches, recent technological advancements in separation, purification, and structural identification have further facilitated the discovery and characterization of these metabolites, expanding the pool of potential bioactive molecules for research and application. We also detail common methodologies for investigating endophyte metabolites, such as fermentation optimization and biotransformation, and briefly touch on how these strategies have been widely adopted to enhance metabolite production and explore structural modifications. With the deepening of interdisciplinary research involving microbiology, chemistry, pharmacology, and biotechnology, the exploration of endophyte secondary metabolites has entered a more systematic and in-depth stage. Finally, we discuss current challenges in translating these findings into practical applications, including issues related to resource accessibility, production scalability, and comprehensive efficacy evaluation, and outline promising future research directions for drug discovery in the field of medicine, encompassing the excavation of untapped endophytic resources, the optimization of production processes, and the in-depth evaluation of safety and efficacy, so as to better harness their potential for human health and sustainable development.
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