Macromolecular glycopeptides are natural products derived from various sources, distinguished by their structural diversity, multifaceted biological activities, and low toxicity. These compounds exhibit a wide range of biological functions, such as immunomodulation, antitumor effects, anti-inflammatory properties, antioxidant activity, and more. However, limited understanding of natural glycopeptides has hindered their development and practical application. To promote their advancement and utilization, it is crucial to thoroughly investigate the pharmacological mechanisms of glycopeptides and address the challenges in natural glycopeptide research. This review uniquely focuses on the primary biological activities and potential molecular mechanisms of glycopeptides as reported in recent literature. Moreover, we emphasize the current challenges in glycopeptide research, including extraction and isolation difficulties, purification challenges, structural analysis complexities, elucidation of structure-activity relationships, characterization of biosynthetic pathways, and ensuring bioavailability and stability. The future prospects for glycopeptide research are also explored. We argue that ongoing research into glycopeptides will significantly contribute to drug development and provide more effective therapeutic options and disease treatment alternatives for human health.