Nanoscale epitaxy or nanoepitaxy for fabricating macroscopically well-aligned nanoscale heterogeneous interfaces on a Si substrate is demonstrated, combining bottom-up and top-down processes efficiently. TiO 2 sputtered in vacuum was selectively nucleated on the atomically flat surfaces of individual CeO2 nanocubes prefabricated by self-assembly in solution on the substrate, and anatase-type TiO2 was grown after a heat treatment by solid-phase epitaxy to produce tandem nanocrystals with heterogeneous interfaces. The atomic configurations of the tandem nanocrystals fabricated after sputtering and subsequent annealing were determined using high-resolution scanning transmission electron microscopy to characterize the nanoscale heterogeneous interfaces. Sharp heterogeneous interfaces were observed between the anatase TiO2(001) and the CeO2(001) nanocubes, with the TiO2  directions being parallel to the CeO2  directions. This unique nanoepitaxial growth technique will contribute to the development of devices and catalytic materials incorporating functional tandem nanocrystals with nanoscale heterogeneous interfaces.