Metal ions play critical roles in the interaction between deoxyribonucleic acid (DNA) and protein. The experimental research has demonstrated that the Mg2+ ion can affect the binding between transcription factor and DNA. In our work, by full-atom molecular dynamic simulation, the effects of the Mg2+ion on the cyclic adenosine monophosphate (cAMP) response element binding protein (CREB)/cAMP response elements (CRE) complex are investigated. It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg2+ion is added. Hence, an obvious change in the structure of the DNA is observed. Then the DNA base groove and base pair parameters are analyzed. We find that, due to the introduction of the Mg2+ion, the DNA base major groove becomes narrower. A potential mechanism for this observation is proposed. It is confirmed that the Mg2+ ion can enhance the stability of the DNA–protein complex.