Basaltic underplating revealed by lower crustal xenoliths is usually considered to be manifested by younger zircon ages than those of the pre-existing crust and/or Sr–Nd isotopic heterogeneity resulting from mixing between mantle-derived basaltic melts and crust. The Hannuoba mafic lower crustal xenoliths have long been regarded as a typical example of Mesozoic underplating owing to the presence of 80–160 Ma zircons and evolved Sr–Nd isotopic compositions. However, our integrated study shows that most Mesozoic zircons in the Hannuoba mafic xenoliths precipitated from partial melts derived from the ancient lower crust. Although a few young zircons may record Mesozoic underplating, none of the xenoliths are products of Mesozoic underplating. It provides the first direct evidence that some zircons in lower crustal xenoliths could be exotic. The contrasting O–Hf isotopic compositions of Mesozoic zircons from the Hannuoba lower crustal xenoliths allow us to distinguish zircons that were grown from different hydrous melts from those that represent recrystallized pre-existing zircons. This has major implications for geological interpretation of the age diversity commonly observed in deep-seated xenoliths worldwide. Furthermore, at Hannuoba both the ∼1.8 Ga zircon ages from the granulite terrain and most of the 1.8–1.9 Ga zircon ages from a previously reported banded granulite xenolith also reflect metamorphism rather than underplating. It demonstrates that high-grade metamorphism or partial melting of Archean rocks can result in zircons with significantly younger U–Pb and THfDM ages. We infer that some granulite xenoliths previously regarded as products of Paleoproterozoic basaltic underplating from other regions (e.g., the Wyoming craton and the Siberian craton) may actually be remnants or derivatives of the pre-existing Archean lower crust. The large range in Sr–Nd isotopic compositions for various Hannuoba lower crustal xenoliths is unlikely to have resulted from mixing between basaltic melts and crust but was rather inherited from the ancient lower crust. Most of the Hannuoba mafic xenoliths can be best explained as residues left after partial melting of the late Archean lower crust that may be represented by the granulite terrain to produce the voluminous 125–143 Ma intermediate–felsic magmatic rocks. Therefore, young zircon ages and heterogeneous Sr–Nd isotopic compositions are insufficient criteria to infer recent underplating. Combined with literature data, it shows that Archean mafic granulite xenoliths are widespread globally, thus arguing against previous suggestion that mafic granulites from the lower crust of most Archean cratons might have formed from post-Archean basaltic underplating. It is implied that the role of basaltic underplating in the evolution of the lower crust in many regions may need to be re-evaluated.