The diseases caused by disorders in glucose and lipid metabolism have become one of the prevalent health issues, posing a serious threat to human health. Previous studies have shown that food-derived polysaccharides have a certain intervention effect on disorders in glucose and lipid metabolism. This article reviewed the structure-function relationship of food-derived polysaccharides and elucidated their role in regulating glucose and lipid metabolism. Some new evidence suggests that secondary metabolites such as short-chain fatty acids, secondary bile acids, and lipopolysaccharide act as signaling molecules, activating pathways related to glucose and lipid metabolism, alleviating oxidative stress, inhibiting inflammation in the body, and regulating the homeostasis of glucose and lipid metabolism. These results indicated that food-derived polysaccharides have a positive impact on the regulation of glucose and lipid metabolism by improving the gut microbiota environment. On the other hand, gut microbiota disturbance can affect the host’s health through the gut-liver, gut-brain and gut-adipose tissue axes. Therefore, it is speculated that food-derived polysaccharides may intervene in glucose and lipid metabolism through the inter-organ crosstalk between gut, liver, adipose tissue, and nervous system. This essay provides a theoretical basis for the development and utilization of food-derived polysaccharides as prebiotics in intervening disorders in glucose and lipid metabolism.