Granites generated by anatexis are ideal crustal probes to decipher the differentiation processes within deep continental crust. In this study, the successive emplacement of granites, including the porphyries and the coarse-grained granites, was found in the nucleus (the Kongling Complex) of the Yangtze Craton. The porphyries, intruding at 1840 ± 17 Ma (SHRIMP ages), occur as veins and contain phenocrysts of K-feldspar (∼15%), quartz (∼5%), plagioclase (∼4%) and garnet (∼1%) setting in a fine-grained groundmass (∼75%) of K-feldspar, plagioclase, quartz and biotite. The coarse-grained granites, emplacing at 1821 ± 8 Ma (SHRIMP ages), are outcropped as pluton and comprise K-feldspar (∼60%), quartz (∼30%), biotite (∼5%), plagioclase (∼5%). They are similar to A-type granites with relatively high SiO2 (69.2–71.5 wt%, 72.6–74.5 wt%), high Fe2O3T/MgO (21.5–27.7, 5.9–19.5), 104*Ga/Al ratios (3.6–4.3, 2.7–3.5) respectively and enriched HFSEs (Th, U, Pb, Ga). The porphyries contain higher total trace element contents and zirconium saturation temperature (mean 892 °C) than those of the coarse-grained granites (mean 803 °C). Magmatic zircons from the porphyries and coarse-grained granites have εHf(t) values of −17.6 to −11.7 and −21.0 to −14.8, which yield two-stage Hf model ages of 3.6–3.3 Ga and 3.8–3.4 Ga respectively, both falling into the evolutionary trend of the 2.9–2.8 Ga Kongling TTGs. It implies both granites are anatectic (crustal reworking) derivatives from partial melting of the Archean TTGs under sustaining extension in Paleoproterozoic. Applying trace element modelling, we further identify a unique tonalitic source for both granites which is analogous to the exposed natural Kongling tonalite, and find the porphyries slightly affected by the juvenile crust. Based on the intrusion of porphyry veins into granitic gneisses, we envisage the crustal structure beneath the craton is layered from older (∼2.94 Ga) tonalites upward to younger (∼2.87 Ga) granitic gneisses. Such hierarchical structure could shed new light on the imperceptible vertical differentiation process as cratonization.