The Qiongjiagang pegmatite-type Li deposit is closely associated with tourmaline-muscovite granite, barren pegmatite and spodumene pegmatite. Zircon and apatite from the Qiongjiagang Li deposit have been studied to characterize textural and compositional changes during magmatic differentiation, fluid exsolution and hydrothermal alteration. Two types of zircon have been identified in all types of granite and pegmatite. Magmatic zircon I is homogeneous or shows weak oscillatory zonation in backscattered electron images and is characterized by high concentrations of U (0.33-6.80 wt%), P (154-5387 ppm), Y (546-10,317 ppm), and HREE (265-5358 ppm). Hydrothermal zircon formed by the interaction of magmatic zircon with magmatic fluids (zircon IIa) and non-magmatic late fluids (zircon IIb). Both types of hydrothermal zircon have lower trace element contents and display abundant pores and inclusions of U bearing minerals uraninite, monazite (only in zircon IIa) and xenotime. High U contents in primary magmatic zircon reflects the overall high-U contents of these highly evolved magma and the absence of other U-phases crystallizing during magmatic differentiation before the crystallization of zircon. Uranium, P, Y, and REE were redistributed during the interaction between magmatic fluid and magmatic zircon. With time, the high U contents resulted in metamictization of zircon. Alteration of the metamict (or magmatic) domains during a later event, unrelated to the emplacement of the mineralized pegmatites, resulted in similar textures as the interaction of zircon with magmatic fluids. In contrast, alteration of apatite by magmatic fluids redistributed mainly Mn, Y, and REE. The textures and chemical compositions both allow to trace fluid exsolution reliably. As separation of late-magmatic fluid is essential for metal enrichment and the formation of rare element pegmatites like for the Qiongjiagang spodumene pegmatites, distinction of the two alteration types is essential to assessing the potential of highly evolved granitic systems to develop mineralization.