Our understanding of crust–mantle differentiation is hampered by the large uncertainty in the composition of the inaccessible lower continental crust. The lower-crustal estimates derived from granulite terrains are compositionally much more evolved than those based on granulite xenoliths and there is no consensus on the origin of the compositional discrepancy. Here an integrated study of granulite terrains, granulite xenoliths and lower crustal–derived magmatic rocks from the Zhangjiakou region of the northern North China craton and a combination of geochronological, mineralogical, geochemical and geophysical data enable us to establish a complete Archean lower crustal cross-section for the first time. It shows that the late Archean lower crust beneath the North China craton is layered, with an intermediate upper lower crust and a mafic lowermost crust. The tonalite–trondhjemite–granodiorite (TTG)-dominated granulite terrains may merely represent the upper lower crust. Our results successfully solve the long-standing question regarding the compositional difference between granulite terrains and xenoliths. It is inferred that a layered Archean lower crust persists in many other cratons (e.g., the Siberian, Slave, Superior, and Tanzanian cratons) and it has an overall composition different from current lower crustal estimates. We further show that the Archean mafic lower crust is temporally coupled with the upper crust. This finding is significant as it raises an important question whether the mafic lower crust and exposed TTGs are genetically linked, which may be a key to understanding crust generation and differentiation processes.