Abstract We review the evolution of late Cenozoic magmatism in the NE Japan arc, and examine the relationship between the magmatism and the crust–mantle structure. Recent studies reveal secular changes in the mode of magmatic activity, the magma plumbing system, erupted volumes and magmatic composition associated with the evolution of crust–mantle structures related to the tectonic evolution of the arc. The evolution of Cenozoic magmatism in the arc can be divided into three periods: the continental margin (66–21 Ma), the back-arc basin (21–13.5 Ma) and the island-arc period (13.5–0 Ma). Magmatic evolution in the back-arc basin and the island-arc periods appears to be related to the 2D to 3D change in the convection pattern of the mantle wedge related to the asthenosphere upwelling and subsequent cooling of the mantle. Geodynamic changes in the mantle caused back-arc basin basalt eruptions during the back-arc basin opening (basalt phase) followed by crustal heating and re-melting, which generated many felsic plutons and calderas (rhyolite/granite phase) in the early stage of the island-arc period. This was followed by crustal cooling and strong compression, which ensured vent connections and mixing between deeper mafic and shallower felsic magmas, erupting large volumes of Quaternary andesites (andesite phase).