Cu2−x Se nanoparticles (Cu2−x Se NPs) as a new therapeutic drug platform is widely used in disease treatment due to their strong near-infrared optical absorption. In recent years, with their continuous expansion of applications in different fields, their own biological effects have received increasing attention. However, little is known about the effect of Cu2−x Se NPs on cancer cell. In this research, we found that Cu2−x Se NPs inhibited proliferation of HepG2 cells (IC50: 15.91 μM) and SMMC-7721 cells (IC50: 43.15 μM) and they mainly induced cell cycle arrest at the G2/M phase. Moreover, Cu2−x Se NPs inhibited HepG2 and SMMC-7721 cell migration and lamellopodia formation. Further studies indicated that Cu2−x Se NPs impaired mitochondrial respiration by inhibiting electron transport chain complex activity, thus reducing adenosine triphosphate levels. The insufficient energy supply subsequently impaired actin cytoskeleton assembly, ultimately inhibiting HepG2 and SMMC-7721 cell proliferation and migration. These findings suggest that Cu2−x Se NPs may have potentially antitumor activity, which might provide new insights of NPs into specific cancer treatment.