The electrochemical quartz crystal microbalance (EQCM) and density functional theory (DFT) have been combined to study the special reaction between thiourea (TU) and metal cluster and the mechanism of the replacement of Cu by Sn in the presence of TU for the first time. The natural bond orbital (NBO) charge of the top copper atom obviously shifts toward positive values compared to the interaction behavior of single and double (SdC) regions with Cu4 cluster via the DFT method. This can explain the reason for the accelerating corrosion process at higher TU concentrations since the copper atoms can change to cuprous ions in this process. It is proven that the thermodynamically impossible replacement of Cu by Sn can occur in the presence of TU by reducing the OCP of the copper electrode to a more negative value than the redox potential of Sn2+/Sn. The DFT investigation on the interactions between delocalization (SdC) and (NsC) regions in TU and Cu4 or Sn4 cluster indicates that the highest molecular occupied orbital (HOMO) of the SdC region has better than adequate to the lowest unoccupied molecular orbital (LUMO) of Cu4 cluster than that of Sn4 cluster. The replacement mechanism deduced based on the first-principles analysis is universally applicable to the alloy deposition, corrosion inhibition, and surface treatment.