Large granitoid batholiths contain key information about the formation and evolution of the continental crust, but their growth mechanism and compositional diversity are still not clear. The Neoproterozoic Huangling batholith, one of the largest granitoid batholith in South China, comprises several plutons and covers an area of ∼ 970 km². The largest trondhjemitic pluton was emplaced at ca. 840 Ma, and its magmatic zircons show large variable Th/U ratios (0.22–1.81) that are strongly correlated with Ti-in-zircon temperatures, zircon U/Yb and Ce⁴⁺/Ce³⁺ ratios. These zircons have negative εHf (−28.3 to −14.6), variable δ¹⁸O (4.43–6.99 ‰) and δ⁹⁴Zr values (−0.38 ‰ to + 0.21 ‰), as well as moderate zircon saturation temperatures (716–771 °C) and high fO₂ (FMQ+1.9). The trondhjemite is therefore proposed to have been derived from the Archean amphibolitic crust and underwent fractional crystallization of zircon, magnetite, apatite and/or titanite. In comparison, one smaller granitic pluton was emplaced at 831 ± 5 Ma. The magmatic zircons have more radiogenic εHf (−11.7 to −10.4), constant δ¹⁸O (6.09–6.66 ‰) and δ⁹⁴Zr values (−0.31 ‰ to + 0.06 ‰), and they have slightly higher zircon saturation temperatures (767–803 °C) and fO₂ (FMQ+2.9). These geochemical features suggest that the granite was derived from a crustal source with mixed juvenile mafic materials and Archean amphibolitic rocks, and did not experience significant fractional crystallization. The Huangling granitoid batholith was formed by multiple injections of felsic melts with the compositional diversity that probably resulted from heterogeneous protoliths and complex magmatic processes in a prolonged magma evolution system.