Obtaining reliable petrochronological and geochemical data from metamict zircon may be challenging. Metamict zircon and crystalline apatite from the Meiwu granodiorite and its microgranular enclaves from the Paleo-Tethys belt are examined to constrain their crystallization ages and the genetic mechanism of related skarn mineralization. The metamict zircon yields highly disturbed Pb-206/U-238 dates. Transmission electron microscopy shows that radiation damage forms nanoscale-banded damaged zones, leading to spurious dates. The coexisting apatite has not accumulated radiation damage, and apatite crystals from the granodiorite and its enclaves yield reasonably precise LA-ICPMS U-Pb Tera-Wasserburg concordia lower intercept dates of 240.2 +/- 3.8 and 239.9 +/- 4.0 Ma (2 sigma), with MSWDs of 1.0 and 2.1. Considering the fast cooling of the granite, the U-Pb dates effectively represent crystallization ages for these rocks. Compositional analysis shows that there are no Ce anomalies in apatite in either the granodiorite or enclave, indicating low oxygen fugacities. Apatite crystals from enclaves have weaker negative Eu anomalies, higher Sr, and lower HREE and Y contents than those in granodiorite. The compositions confirm enclaves as products of water-rich melts, resulting in amphibole fractionation and suppression of plagioclase crystallization. The hydrous magma induced production of hydrothermal-fluids that mobilized metals dispersed in dry magma and concentrated them into mineralization traps, which contributed to the formation of widespread skarns in Paleo-Tethys belt. This study demonstrates that apatite is effective in tracing the evolution of magmatic systems containing metamict zircon.