Microalgae, as an important biological resource, have garnered increasing attention from both academia and industry in the global trend toward healthy diets due to their abundance in various high-value bioactive compounds. Microalgae are rich in bioactive compounds, including phycobiliproteins, polyunsaturated fatty acids, vitamins, carotenoids, and polysaccharides, and exhibit remarkable antioxidant, anti-inflammatory, and immunomodulatory effects. In recent years, microalgae and their bioactive components have been increasingly recognized for their potential to promote gastrointestinal health by enhancing gut barrier function, modulating the gut microbiota, and suppressing intestinal inflammation. The composition and characteristics of major bioactive components in common microalgae, such as Spirulina and Chlorella, are systematically reviewed in this paper. Their mechanisms of action in improving gastrointestinal function are comprehensively discussed, along with their potential roles in preventing gut-related diseases and promoting overall health. These findings provide theoretical support and scientific guidance for the development of functional foods and dietary supplements. In the future, with advances in extraction processes and in-depth research into their mechanisms of action, microalgae and their bioactive compounds are expected to play an increasingly important role in health.