A large Nb–Ta ore deposit was found in the Yushishan leptynite in the west Qilian Orogenic Belt (QOB). Based on a field geological survey and using a Mineral Liberation Analyser (MLA, including scanning electron microscopy (SEM) and energy-dispersive spectrometer (EDS)) methods, eight Nb minerals (fergusonite, polycrase, columbite, Nb-rutile, aeschynite, pyrochlore, microlite, and ilmenorutile) were found to occur in the leptynite. This accounted for approximately 69% of Nb, with fergusonite, polycrase, and columbite being the dominant phases. The other 17.90% Nb as a minor element was dispersed in titanium magnetite–maghemite, and another 13.00% Nb was dispersed in gangue minerals. Nb minerals are formed mainly by two metallogenesis stages. The first stage is magmatic genesis to form four Nb minerals, euhedral-subhedral fergusonite, polycrase, pyrochlore, and microlite, which are crystallized within or between primary minerals, such as quartz and feldspar. Late alteration phenomena are locally observed. The second stage is the hydrothermal genesis of columbite, anhedral fergusonite, Nb-rutile, and aeschynite, which are dispersed in the fissures of the wall rocks as irregular veins and lump assemblages. Meanwhile, they are closely associated with metasomatic chlorite, albite, and secondary quartz. Furthermore, direct metasomatism among different Nb minerals is also found at the local scale. The Nb percentage of these two Nb mineral mineralization types is approximately equal, which reflects two main mineralizing periods. The first stage of mineralization occurred in the Neoproterozoic Era (834–790 Ma). Magmatism of this period produced early niobium and formed fergusonite, polycrase, pyrochlore, microlite, and zircon. The initial enrichment of Nb, Ta, and other rare metals occurred during this stage. The second stage of mineralization occurred in the Caledonian period (490–455 Ma). Large-scale and intense tectonic–magmatic thermal events occurred in the western part of the QOB due to the plate subduction and convergence (510–450 Ma). Hydrothermal activity in this period formed columbite, fergusonite, Nb-rutile, and aeschynite. Moreover, rare metal elements in the Nb-bearing rocks activated and migrated at short distances, forming in situ Nb–Ta-rich ore deposits.