The increasing prevalence of obesity is becoming a global health concern due to its association with chronic diseases including type 2 diabetes, non-alcoholic fatty liver disease, and cardiovascular diseases. Obesity occurs when energy intake outweighs energy expenditure, leading to a conventional intervention strategy being “eat less and move more.” However, this strategy does not consider the influence of genetic factors and their interactions with environmental factors (diets and physical activity), making obesity prevention and management inefficient. To better understand obesity, research in nutrigenetics and nutrigenomics seek to explore the influence of genetic variations on dietary responses, and how dietary components alter gene expression in obese individuals. Current evidence suggests that variations in genes involved in lipid regulation, carbohydrate metabolism, and energy homeostasis are strongly associated with the risk of obesity and its related metabolic syndromes. In addition, diet-gene interactions influence intervention effectiveness for obesity management. By examining obesity-related metabolic pathways, we can reveal the functional basis of diet-gene interactions in relation to obesity risk. Although limitations exist within the current literature, emerging evidence indicates that obesity risk and intervention can be affected by diet-gene interactions, and continued research is needed for further exploration.