Metabolic disorders may cause many complications, including disruption of blood glucose, blood lipids, and uric acid levels, thereby posing a serious threat to human health. Berberine (BBR) is a natural isoquinoline alkaloid widely present in a variety of medicinal plants. Studies have suggested that BBR plays a role in metabolism-related functions, such as glycolipid, mitochondrial energy, and bone metabolism. BBR has been shown to effectively regulate metabolic responses in a variety of target cells including intestinal cells, liver cells, and adipocytes. Multiple signaling pathways and networks are involved in this process, such as the AMPK/SIRT1, PI3K/AKT/mTOR, Wnt/β-catenin, and iPLA2β/CL/Opa1 pathways, which are essential for cell proliferation, differentiation, apoptosis, autophagy, and signal transduction. Therefore, BBR may be a promising drug for the regulation of metabolic disorders and treatment of metabolism-related diseases. However, the underlying mechanisms and effects on key cells involved in metabolic processes are complex and unclear. This paper reviews the research on the regulation of various metabolic processes by BBR, focusing mainly on the effect on key target cells, and discusses the existing blind spots and future research directions for the development of the medicinal and clinical value of BBR in the future.