Magmatic–hydrothermal evolution plays a key role in the formation of peralkaline rocks and associated zirconium and rare earth element (REE) mineralization. Zircon is a common mineral in peralkaline rocks and can record invaluable information about the magmatic–hydrothermal evolution of these systems. To help better constrain the magmatic–hydrothermal evolution of and Zr enrichment processes in peralkaline systems, we characterized the mineralogy and geochronology of a texturally complex zircon megacryst from the rare metal mineralized Yilanlike nepheline pegmatite in the South Tianshan. Here we present laser Raman spectra, in situ elemental data, and U–Pb geochronological data for the zircon megacryst to constrain the age and magmatic–hydrothermal evolution of this nepheline pegmatite. Three types of zircon domains (Zrn-I, Zrn-II, and Zrn-III) are distinguished based on their morphological and geochemical characteristics. Zrn-I has well-developed oscillatory zoning, REE patterns similar to magmatic zircon, high Th/U ratios (0.09–0.47), and concordant U–Pb ages, indicative of a magmatic origin. Zrn-II is characterized by weak oscillatory and patchy zoning, low full width at half maximum (FWHM) values (6.58–14.86 cm−1), and low trace-element contents (e.g., Nb = 0.16–0.92 ppm, Ta = 0.13–0.54 ppm, U = 195.77–812.92 ppm, Th = 15.85–158.95 ppm, and total REE = 13.00–187.75 ppm), indicative of a recrystallized origin as this process generates heterogeneous zoning, heals the zircon crystal lattice, and lowers trace-element contents. Concordant U–Pb ages and low Th/U ratios (0.05–0.26), combined with moderate Ce/Ce* and (Sm/La)N ratios (0.38–33.96 and 1.34–27.73, respectively), which are characteristic of the magmatic–hydrothermal transition, indicate that Zrn-II recrystallized in the presence of hydrothermal fluids. Zrn-III is characterized by “spongy” textures, thorite inclusions, high FWHM values (6.58–47.87), relatively high contents of total REE (14.79–962.05 ppm), and discordant U–Pb ages, suggestive of an origin related to the hydrothermal alteration of earlier zircons. Results of U–Pb dating of Zrn-I and -II yield weighted concordant ages of 286.9 ± 1.9 Ma (MSWD = 1.5, n = 23) and 279.3 ± 2.3 Ma (MSWD = 0.24, n = 20), respectively, whereas the U–Pb results for Zrn-III are largely discordant. Based on these textural, geochemical, and geochronological results, a multi-stage process for the formation of the zircon megacryst and nepheline pegmatite is proposed. First, the parent magma of the nepheline pegmatite was emplaced and the zircon megacryst crystallized at ca. 286.9 Ma (represented by Zrn-I). As the magma differentiated, hydrothermal fluids derived from the evolved magma recrystallized Zrn-I to Zrn-II at ca. 279.3 Ma. Finally, a second hydrothermal event altered Zrn-I and -II to form Zrn-III. Given the low concentrations of UO2, ThO2, and Y2O3 in Zrn-II, and the CHARAC behavior of Zr and Hf, the fluid that formed this zircon variety likely had relatively low F contents. This multi-stage magmatic–hydrothermal evolution likely played an essential role in concentrating Zr and generating the Zr mineralization. Zirconium is primarily enriched via magmatic crystallization, as illustrated by the high abundances of Zrn-I in the Yilanlike nepheline pegmatite. The presence of hydrothermal zircon (Zrn-II and Zrn-III) suggests that hydrothermal recrystallizatio nay have also facilitated the enrichment of Zr. It is, therefore, suggested that both magmatic and hydrothermal processes contributed to the enrichment of Zr in the Yilanlike nepheline pegmatite.