Metabolic syndrome, a major health issue, is closely associated with gut microbiota dysbiosis, defined by an imbalance of beneficial and harmful bacteria. This imbalance contributes to various gastrointestinal and metabolic disorders. The current research highlights the effectiveness of natural plant components, especially dietary fibers and polyphenols, in positively influencing gut microbiota composition. Sea buckthorn, rich in polyphenols, has emerged as a key player in regulating gut microbiota and mitigating metabolic inflammation. This chapter examines how sea buckthorn and other treatments targeting gut microbiota impact metabolic diseases like obesity, non-alcoholic fatty liver disease, diabetes, and cardiovascular disease. It also explores the mechanisms of sea buckthorn in addressing metabolic disorders, focusing on lipid metabolism proteins and oxidative stress markers. This comprehensive review underscores the potential of sea buckthorn as a natural intervention strategy for various chronic metabolic diseases. By influencing gut microbiota composition and diversity, sea buckthorn holds promise in maintaining intestinal barrier integrity, reducing inflammation, and ultimately contributing to metabolic health.