Plant polyphenols and polysaccharides exhibit a range of biological activities, such as antioxidant, anticancer, hypoglycemic, and immunomodulatory effects. However, the bioavailability of polyphenols is often hindered by challenges during digestion, such as poor intestinal absorption and limited systemic availability. Recent research has shown that polyphenols can form stable complexes with polysaccharides through molecular interactions, which not only enhance the solubility and gastrointestinal stability of polyphenols but also improve their functional properties in combination with polysaccharides. This review systematically examines the mechanisms underlying the formation of polyphenol-polysaccharide complexes, focusing on both non-covalent and covalent binding interactions. The regulatory effects of these molecular interactions on the following four key areas have been thoroughly discussed: enhancement of polyphenol bioavailability (through improved solubility and stability); improvement of polysaccharide functional properties (including viscosity, crystallinity, rheological properties, emulsifying capacity, and stability); synergistic biological activities of the complex system (such as antioxidant and anti-inflammatory as well as regulation of glucose and lipid metabolism); and impact on gut homeostasis (including gut microbiota composition, microbiota-derived metabolites, and gut barrier integrity). This study provides a novel approach and theoretical framework for the development of precision nutrition delivery systems based on polyphenol-polysaccharide molecular interactions as well as the development of functional food ingredients.