The gut microbiota plays a pivotal role in maintaining host metabolic homeostasis. Accumulating evidence has demonstrated that dysbiosis of the gut microbiota is closely associated with metabolic disorders, including obesity, type 2 diabetes mellitus (T2DM), and non-alcoholic fatty liver disease (NAFLD). These alterations affect energy harvest, bile acid and short-chain fatty acid metabolism, intestinal barrier integrity, and low-grade inflammation, thereby contributing to insulin resistance and ectopic fat accumulation. In this narrative review, we summarize current knowledge on microbiome-host interactions in metabolic diseases, with a focus on energy metabolism, immune regulation, and inflammatory pathways. We further discuss the therapeutic potential and limitations of microbiota-targeted interventions, such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation (FMT), highlighting the heterogeneity of clinical responses and safety considerations. Finally, we outline emerging precision strategies and future research directions aimed at integrating multi-omics profiling and patient stratification to inform personalized prevention and treatment of metabolic diseases.