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The global prevalence of obesity has nearly tripled in the past 40 years and continues to rise at an alarming rate. High fat and high carbohydrate diets can cause gut microbiota disturbance and impairment of intestinal barrier function in obese individuals. Dysbiosis of the gut microbiota and its metabolites crossing the intestinal barrier lead to insulin resistance, imbalance in energy metabolism, reduced fat browning capacity and increased levels of inflammatory factors, which in turn induce chronic diseases such as diabetes, hypertension and cardiovascular diseases. In this paper, the molecular mechanism of obesity mediated by the gut microbiota is systematically elucidated. Based on this, we propose that the intestinal microecology can be regulated by supplementing probiotics and prebiotics or by changing lifestyle and dietary pattern, which in turn will help to prevent and control obesity.