Thorium deposit related to alkaline/peralkaline magmatism is the dominant thorium source. Its ore-forming thorium mechanism has long been fascinating. The Younusisayi Th deposit, hosted in early Paleozoic alkali-feldspar granite in the South Altyn Complex, NW China, is an example to explore the Th mineralization processes in magmatic-hydrothermal systems. Zircon U-Pb dating shows that the ore-hosting alkali-feldspar granites are emplaced at 445.7–439.0 ± 1.3 Ma. The apatite that occurs concomitantly with thorite in the mineralized alkali-feldspar granites formed at are 442.0–438.0 ± 14 Ma, indicating Th mineralization temporally related to the magmatism. Four populations of fluorite exhibit distinct occurrences, the fluorite Ia and Ib are in intergrowth with thorite, but the fluorite IIa and IIb are not. Notably, four populations of fluorite are differentiated by their Th + U and HREE concentrations, fluorite Ia and Ib show higher Th + U contents and lower HREE contents than fluorite IIa and IIb. Th was extracted by magma during emplacement. As a strong incompatible element, thorium will not be enriched in rock-forming minerals. In the process of magmatic evolution, thorium is gradually enriched in the post-magmatic fluids which contains abundant volatile components. Thorium can be transported as F-Th complexes in F-rich fluids. As temperature decreased, thorium precipitated in the form of thorite, and fluorite Ia and Ib crystallized with a low HREE content. Fluorine from the decomposition of F-Th complexes, reacts with HREE in the fluids to form F-HREE complexes, which increases the HREE content in the fluid. Therefore, the fluorite IIa and IIb which formed in the late stage of mineralization have obviously higher contents of HREE. We propose that the Younusisayi deposit, with an average grade of 0.4 wt% ThO2, formed in a post-collisional extensional environment during the early Paleozoic. The Younusisayi deposit is best classified as a magmatic-hydrothermal deposit. Our results demonstrate the usefulness of geochemistry of fluorite for tracing the ore-forming process, thus establishing the ore formation model.