The Permo-Triassic Jomda-Weixi-Yunxian continental margin arc belt in the southeastern Tibetan Plateau was formed by the subduction of the main Paleotethyan branch underneath the Cathaysian-affinity blocks along the Longmu Co-Shuanghu-Changning-Menglian suture. This belt consists of three segments with distinctive magmatism history. Available geochronological data revealed that the northern and southern segments of this belt comprise several volcanic successions intercalated with terrestrial clastics suggesting long-lived and pulsed magmatism. In contrast, the middle segment is made of a single volcanic pile of dacite/rhyolite and minor basalt with thickness of >1.6km. Numerous granodiorite batholiths and a few diabase dykes intruded the volcanic pile. Detailed zircon U-Pb dating indicates that the volcanic rocks and intrusive rocks were formed during a short time period of ~7millionyears (~244–251Ma), defining a magmatic flare-up. Petrographic and geochemical data including Sr-Nd isotopics demonstrate that the felsic magmas were derived from ancient crust, while the basalt and diabase are sourced from the mantle wedge induced by subduction of the Paleo-Tethys. Structural studies reveal syn-subduction crustal shortening and thickening of the middle segment. The thickened crust likely has prevented the subduction-induced basaltic magma from eruption; they alternatively were accumulated in the bottom of the crust yielding a magma chamber. The chamber heated, softened, and melted the crust, forming felsic magmas. When the crust was weakened to a critical threshold, the felsic magmas rose up and erupted to the surface, resulting in the magmatic “flare-up”. This study suggests that syn-subduction shortening and thickening of the overriding crust seems to have played a significant role in the development of magmatic flare-ups along a continental margin arc-system. Other well-studied examples include the Mesozoic Serra Nevada and the late Miocene to Holocene Altiplano-Puna Plateau, central Andes.