In this study, the modulatory effect of capsaicin (CAP) on the circadian rhythm of glucose metabolism in the liver and pancreas of mice fed a high-fructose and high-fat diet (HFFD) was investigated. Our results indicated that CAP alleviated HFFD-induced insulin resistance and increased liver glycogen content in mice. In addition, it restored the rhythmic expressions of circadian clock genes and glucose metabolism-related genes in the liver and pancreas, alleviated pancreatic dysfunction and reprogrammed the fecal metabolic profile of HFFD-fed mice. These findings suggested that CAP might work as a functional food ingredient to improve the circadian rhythm of glucose metabolism, providing a more effective dietary intervention strategy for the prevention of metabolic disorders and circadian rhythm disturbances.