The mammalian circadian clock precisely controls various physiological processes, including energy metabolism, to help the body adapt to the diurnal light–dark cycles induced by the earth autorotation. Although the clock and metabolism are tightly coupled and interacted, the molecular mechanism through which these two pathways are integrated remains largely unknown. In the past 10 years, we have been focusing on this important scientific question and innovatively proposed three integration modes, including the ‘parallel connection’ mode orchestrated by nuclear factors, the ‘serial connection’ mode orchestrated by clock-controlled proteins, and the ‘combinational connection’ mode regulated by metabolites. Here, we summarize and discuss the molecular mechanisms of the integration between peripheral circadian clock and energy metabolism in metabolic tissues.