The copper (Cu)/tantalum (Ta) nanofilms are the vital component in the through silicon via (TSV) wafer. However, the current lack of research on the ultra-precision machining of Cu/Ta nanofilms limits the development of TSV-based 3D integration technologies. In this work, molecular dynamics simulations are conducted to reveal the microstructure and interface evolution mechanism of Cu/Ta nanofilms during nano-grinding under various grinding depths. The results show that the material removal mode differs between the Cu and Ta layers, and the thickness of the subsurface damage layer of the Cu layer is greater than that of the Ta layer. The Cu/Ta interface is well stabilized, and small amounts of micro-defects appear only at larger grinding depths after grinding. The lattice mismatch of the constituent layers and the hindering role by the interface lead to stress concentration at the interface, and it is more obvious with increasing grinding depth. Nevertheless, there is a significant stress release after grinding. Our computations indicate that the competition between the evolution of interfacial structures and discrepancies in the physical properties of constituent layers leads to an increase in grinding forces at the interface. Furthermore, the heat transfer is obstructed by the Cu/Ta interface. This study provides valuable insights into the grinding mechanisms of Cu/Ta nanofilms, which is conducive to further improving the manufacturing process of the TSV wafer and enhancing the performance of microelectronic devices.