The large volumetric variations experienced by metal selenides within conversion reaction result in inferior rate capability and cycling stability, ultimately hindering the achievement of superior electrochemical performance. Herein, metallic Cu2Se encapsulated with N-doped carbon (Cu2Se@NC) was prepared using Cu2O nanocubes as templates through a combination of dopamine polymerization and high-temperature selenization. The unique nanocubic structure and uniform N-doped carbon coating could shorten the ion transport distance, accelerate electron/charge diffusion, and suppress volume variation, ultimately ensuring Cu2Se@NC with excellent electrochemical performance in sodium ion batteries (SIBs) and potassium ion batteries (PIBs). The composite exhibited excellent rate performance (187.7 mA h g−1 at 50 A g−1 in SIBs and 179.4 mA h g−1 at 5 A g−1 in PIBs) and cyclic stability (246.8 mA h g−1 at 10 A g−1 in SIBs over 2500 cycles). The reaction mechanism of intercalation combined with conversion in both SIBs and PIBs was disclosed by in situ X-ray diffraction (XRD) and ex situ transmission electron microscope (TEM). In particular, the final products in PIBs of K2Se and K2Se3 species were determined after discharging, which is different from that in SIBs with the final species of Na2Se. The density functional theory calculation showed that carbon induces strong coupling and charge interactions with Cu2Se, leading to the introduction of built-in electric field on heterojunction to improve electron mobility. Significantly, the theoretical calculations discovered that the underlying cause for the relatively superior rate capability in SIBs to that in PIBs is the agile Na+ diffusion with low energy barrier and moderate adsorption energy. These findings offer theoretical support for in-depth understanding of the performance differences of Cu-based materials in different ion storage systems.