The Nb-Ta ore body in the Shihuiyao Rb-Nb-Ta-(Be-Li) deposit comprises muscovite-albite granite (MAG) and greisen (GR), with the dominant Nb-Ta minerals of columbite-group minerals (CGM) and ixiolite. The petrographic and chemical data suggest that the Nb-Ta oxides well record the magmatic-hydrothermal evolution process. The magmatic CGM are generally homogenous crystals or with oscillatory zoning patterns, while the CGM formed during the magmatic-hydrothermal transition stage overprints the early CGM crystals in the MAG or shows a normal zoning pattern (decreasing Nb/Ta ratios from the core to rim) in the GR, and possesses higher contents of Sc and Ti. The hydrothermal Nb-Ta oxides in both the MAG and GR share the same origin, i.e., the hydrothermal fluids exsolved from the magma at the late stage of magmatic evolution. However, distinct chemical differences between them indicate that a single fluid activity did not pervade the entire system; instead, two different hydrothermal processes were present: fluid metasomatism and water–rock reaction. The hydrothermal CGM generally occurs in the GR and metasomatizes the primary crystals by a coupled dissolution-reprecipitation mechanism. The chemical compositions of these CGM grains were significantly modified during this process, which was manifested by the increasing Sn and W contents in the reprecipitated phases. The ixiolite is most likely formed by another hydrothermal mechanism, i.e., water–rock reaction, during which the hydrothermal fluids can extract a large amount of Sn, Sc, U, and REE from the wall rocks or earlier formed magmatic phases and finally controlled the formation and chemical distribution of the ixiolite.