The petrogenesis of the isolated pegmatites from granites is under debate. In the Chinese Altai, massive isolated pegmatites have been regarded as derivatives of granitic melts, which contradicts to the results of recent studies. In this work, the geology and mineralogy, as well as the zircon U-Pb chronology and Hf isotope geochemistry, of 10 Permian pegmatites are analyzed, and a comparative study of the Permian pegmatites and granites is conducted to reveal the petrogenesis of the Permian pegmatites in the Chinese Altai. The Permian pegmatites are concentrated in the Qiongkuer domain with a linear distribution and show structural control from regional anticlinoriums and connections to adjacent migmatites and luecogranite dykes. Their zircon U-Pb ages are 274-253 Ma, with the dominating age being late Permian. The pegmatites have three mineralization types including Li-Be-Ta-Nb +/- Sn, Be-Nb-Ta +/- REEs (rare earth elements) and REEs. The former two are comparable with the Triassic and Devonian-Carboniferous pegmatites in mineralization and Hf isotope composition, respectively, and the latter is unique in the Permian generation. The Permian pegmatites have comparable Hf isotope compositions with the juvenile and specific components in the Habahe Group, which indicates the dependency of mineralization on source from the heterogeneous Habahe Group metasedimentary rocks. The pegmatites also show decoupling spatial-temporal and differentiation-source correlations with the Permian granites, indicating no genetic relationship between them. Combining with the Permian high temperature metamorphism and previous tectonic-magmatic-metamorphic studies, we suggest that the Permian rare metal/earth pegmatites were likely generated by anatexis of the Habahe Group metasedimentary rocks under an extensional setting after the arc-arc collision between the Junggar arcs and the Chinese Altai. (C) 2020 Elsevier B.V. All rights reserved.