Layered materials have received extensive attention for widespread applications such as energy storage and conversion, catalysis, and ion transport owing to their fast ion diffusion, exfoliative feature, superior mechanical flexibility, tunable bandgap structure, etc. The presence of large interlayer space between each layer enhances intercalation of the guest ion or molecule, which is beneficial for fast ion diffusion and charge transport along the channels. This intercalation reaction of layered compounds with guest species results in material with improved mechanical and electronic properties for efficient energy storage and conversion, catalysis, ion transport, and other applications. This review extensively discusses the intercalation of guest ionic or molecular species into layered materials used for various types of applications. It assesses the intercalation strategies, mechanism of ionic or molecular intercalation reactions, and highlights recent advancements. The electrochemical performances of several typical intercalated materials in batteries, supercapacitors, and electrocatalytic systems have been thoroughly discussed. Moreover, the challenges in the design and intercalation of layered materials, as well as prospects of future development are highlighted.