This paper studies the structural evolution of (AgCo)201 clusters with different Co concentrations under various temperature conditions by using molecular dynamics with the embedded atom method. The most stable position for Co atoms in the cluster is the subsurface layer at low temperature (lower than 200 K for the Ag200Co1 cluster). The position changes to the core layer with the increase of temperature, but there is an energy barrier in the middle layer. This makes the Ag-Co cluster form an Ag-Co-Ag three-shell onion-like configuration. When the temperature is high enough [higher than 800 K for (AgCo)201 clusters with 50% Co], Co atoms can obtain enough energy to overcome the energy barrier and the duster forms an Ag-Co core-shell configuration. Amorphization for the onion-like and core-shell clusters is induced by the large lattice misfit at Ag-Co interfaces. The structural evolution in the Ag-Co cluster is related to the release of excess energy.