The Lesser Qinling area is the largest outcrop of the Precambrian basement in the southern margin of the North China Craton (S-NCC). Notably, many carbonatite-related polymetallic deposits are distributed in this area, including the Jialu deposit with light and heavy REE mineralization. Carbonatite and granite from the Jialu deposit contain diverse monazite and zircon grains, and deciphering the age distributions and chemical compositions of these monazites and zircons is crucial for comprehending the multi-stage magmatic and metamorphic events in the S-NCC. Type I monazite from banded REE ore veins yields a U-Pb age of 217.0 ± 5.0 Ma, representing the formation age of carbonatite. Type II monazite from granite yields consistent U-Pb and Sm-Nd ages of ∼1.95 Ga, representing the emplacement age of granite. Type III monazite is hydrothermal in origin, and yields two dominant age peaks at ∼550 Ma and ∼525 Ma. Types I, II and III zircons are xenocrysts from the Taihua Group and yield two main age peaks at ∼2.35 and ∼2.17 Ga. Of note, type III zircon also records an early Paleozoic tectonothermal event by a lower intercept age of 532 ± 59 Ma, which overlaps the ages recorded by hydrothermal monazite. The early Paleozoic tectonothermal events discovered may be a manifestation of the global Pan-African Orogeny in the S-NCC. This new finding further implies that the S-NCC was significantly affected by the assembly of the Gondwana supercontinent during the early Paleozoic.