The intrinsic assumption of radiogenic isotope tracing is that isotope systems maintain equilibrium between melt and source. However, this assumption is not naturally correct, particularly for S-type granites, which are formed by partial melting of metasedimentary rocks. The S-type metagranites from the North Qinling Terrane show various degrees of HfNd isotope decoupling and discrepancies between whole-rock and zircon Hf isotopes. Zircon UPb dating yields emplacement ages from 946 to 890 Ma. Their high δ18O values, (87Sr/86Sr)i ratios, and negative εNd(t) values overlapped with metasedimentary rocks in the Qinling Group imply that they are derived from partial melting of the Qinling Group. The low Rb/Ba, Rb/Sr, Al2O3/TiO2, and high CaO/Na2O ratios indicate that their sources are metagraywackes. The negative correlation between decoupling degrees of HfNd isotopes and Zr concentrations suggests that the incomplete dissolution of zircon during partial melting results in the decoupling. The discrepancy between whole-rock and zircon Hf isotopes can be attributed to the combined effect of incomplete dissolution of zircons and the release of various Hf isotope compositions from partly dissolved inherited zircons to local melts. The compiled literature data suggest that whole-rock HfNd isotope decoupling of most metagraywacke-derived S-type granites is caused by incomplete melting of zircons, whereas those of metapelite-derived S-type granites may be controlled by both incomplete melting of zircons and source inheritance.