Brain and muscle arnt-like protein 1 (Bmal1) is the core gene of biological clock, which belongs to the transcription factor family of bHLH-PAS (basic helix-loop-helix-per-arnt-sim) domain. It can regulate the circadian rhythm through its own expression and the transcription-translation feedback regulation of the biological clock, which plays an important role in the life activities of organism. The disorder of biological clock induces a series of chronic metabolic diseases, such as cardiovascular diseases, hepatopathy and neurodegenerative diseases, usually accompanied by abnormal expression of Bmal1. Exercise may up-regulate Bmal1 expression in peripheral tissues and organs to improve chronic metabolic diseases. Different exercise loads and types of exercise, such as aerobic exercise, resistance exercise, will lead to the differential expression of Bmal1. There are many potential mechanisms of Bmal1 in improving chronic metabolic diseases by exercise intervention, such as reducing inflammation and oxidative stress, regulating autophagy, maintaining mitochondrial quality and function, interacting with exerkines and microRNA. This article reviews the physiological function of Bmal1 in multiple tissues and organs and the relationship between corresponding chronic metabolic diseases, discussing the influence of exercise intervention on Bmal1 expression deeply and putting forward the potential mechanism of Bmal1 in improving chronic metabolic diseases by exercise, in order to provide a new perspective for exercise as a non-drug treatment to prevent and treat chronic metabolic diseases.