The formation of widespread Late Mesozoic magmatic rocks (dominantly felsic rocks) in SE China needs a physical and chemical balance between crustal and mantle melting, which could be reconciled by complicated transcrustal magmatic systems in deep crustal hot zones with time. After the relative magmatic quiescence at ca. 210–180 Ma, magmatic activities were mainly developed in the interior of SE China with an areal distribution and subsequently concentrated in the present coastal area with an overall linear pattern after ca. 140 Ma except the Lower Yangtze region. The spatiotemporal change requires a unique crust-mantle geodynamic coupling with the evolution of deep crustal hot zones from intracontinental to continent marginal setting. Correspondingly, the magmatic rocks show a compositional change from bimodal distribution in Early and Middle Jurassic to unimodal and weakly bimodal pattern in Late Jurassic and Early Cretaceous. In general, most of the Late Mesozoic intermediate to felsic magmatic rocks show higher Mg# than typical rifting-related rocks at given SiO2, which requires the addition of water and possible mass transfer and mixing of underplated hydrous basaltic magma in the deep crustal hot zones. The occurrence of high-Sr/Y and La/Yb rocks and possibly thickened crust (ca. 40 km) before ca. 140 Ma, combined with the current thin crust thickness (ca. 31-33 km) as revealed by seismic data, indicates a widespread crustal thinning after ca. 140 Ma. The relatively thickened crust before ca. 140 Ma is beneficial for melting of underlying old crust that is composed of dominantly Neoproterozoic and Paleoproterozoic components, the formation of porphyritic Cu deposits, the subsequent magmatic differentiation and associated giant W, Sn, Nb, Ta and Li ore deposits. In contrast, the deep crustal hot zones progressively migrated to the present coastal area after ca. 140 Ma, driving the increasing amounts of intermediate rocks and intermediate-felsic volcanic rocks. In general, the diversity and compositional change of Late Mesozoic magmatic rocks and associated ore deposits in SE China may be controlled by the evolution of deep crustal hot zones in different tectonic settings in response to the subduction of Paleo-Pacific Plate.