The structure and thermodynamic properties of Cu-Co alloy cluster with Cu atoms distributed in inner layer and outer surface of Co cluster are investigated by the molecular dynamics simulation combining with an embedded atom potential method. The results demonstrate that there are huge differences in structure, energy and melting point between the inner layer and outer surface of Co clusters due to various doping layers comprised of the same number of Cu atoms. The different doping positions of Cu atoms in Co cluster make atoms shift towards lower energy state. However, after relative movement, the supplementary deposition of subsequent atoms leads to the relatively non-diffusive phase transformation of cluster structure. The segregations of Cu atoms from inner layer to outer surface of Co cluster are the main reason for the enormous difference in melting point between the inner layer and outer surface of Co clusters with the same percentage of Cu atoms.