The Tianshan orogen, in the southern Central Asian orogenic belt, consists of continental fragments stitched together during mid- to late Paleozoic arc magmatism generated by the closure of the paleo–Asian Ocean. Controversy persists regarding the timing of final structural amalgamation of the region and therefore whether Permian magmatism was generated in a subduction or intraplate environment. Based on new field mapping, zircon U-Pb geochronology, and isotope data from the 295–290 Ma Gobi-Tianshan intrusive complex in southwestern Mongolia, we argue that this complex is a voluminous intermediate batholith generated by subduction and that it is related to plutons of similar age and character in Tianshan tectono-magmatic belts to the west. In the study area, as well as in Carboniferous and Permian plutons across the Tianshan, mantle isotopic signatures remain consistently primitive. Permian plutons show an increase in radiogenic Sr with no concurrent decrease in radiogenic Nd, which may be due to the influence of subducting continental sediment in the early Permian. This model explains the transitional nature of magmatic compositions and structures in the Gobi-Tianshan intrusive complex.