Two successive and parallel magmatic arcs within the southern Alxa provide an ideal area to examine the influence of tectonic switching on temporal and spatial distribution of magmatism within accretionary orogens. This study presents new geochronological and geochemical data for Yingen and Quagu plutons from the southern Alxa, located in the southern Central Asian Orogenic Belt. Late Permian Yingen granitic dikes (ca. 252 Ma) have depleted whole-rock Nd isotopic compositions, high Sr, low Y and Yb, and high Sr/Y ratios, all of which indicate they were generated by the partial melting of subducted young/hot oceanic slab. The Middle Permian (271 Ma) Yingen hosting granites contain elevated contents of Nb and Zr, and have high 10,000 × Ga/Al ratios, suggesting that they resulted from mixing between Neoproterozoic crust-derived felsic magmas and depleted mantle-derived mafic magmas. The Quagu pluton yields ca. 271–262 Ma zircon U-Pb ages and has an adakitic high-Mg diorite-like geochemical composition, suggesting that it originated from interaction between slab-derived melts and overlying peridotite material. Collectively, these data record the subduction of the Enger Us oceanic slab beneath Mesoproterozoic–Neoproterozoic sialic crust, generating a Japan-type arc within the southern Alxa during Middle–Late Permian. Temporal-spatial variations of zircon Hf isotope for plutons suggest tectonic switching from advancing to retreating subduction during Carboniferous–Early Triassic within the southern Alxa. An advancing subduction resulted from the subduction of the Paleo-Asian Ocean, and a retreating subduction was related to plate boundary reorganization during the assembly of Pangea.