Sn-based lithium-ion battery (LIB) anodes have a lower risk of lithium dendrite formation and a higher storage capacity of 993 mAh g−1 vs. 372 mAh g−1 compared to carbon-based anodes. Alloying Sn with Cu can reduce the reaction stresses in the anode, and Cu6Sn5 is therefore a promising candidate material to replace carbon-based anodes. However, the separation of Cu during the second stage of the lithiation reaction results in slow kinetics and degrades the cyclability of the anodes. This study proposes an effective method to inhibit the separation of Cu via the addition of Ni. Ni occupies the Cu positions in the Cu6Sn5 crystal structures to form (Cu, Ni)6Sn5, and therefore alters the crystal structure of the anode, leading to the formation of superstructures. As a result, Ni partially blocks the diffusion pathways of Li and therefore inhibits the Cu separation reaction, while the superstructure provides additional Li storage sites to increase the capacity of the anodes. Ni also refines the grain size of Cu6Sn5, leading to faster kinetics. The reaction mechanisms of the modified anodes are confirmed by in-situ synchrotron X-ray powder diffraction and ex-situ high voltage transmission electron microscopy.