In Staphylococcus aureus, vancomycin-resistance-associated response regulator (VraR) is a part of the VraSR two-component system, which is responsible for activating a cell wall-stress stimulon in response to an antibiotic that inhibits cell wall formation. Two VraR-binding sites have been identified: R1 and R2 in the vraSR operon control region. However, the binding of VraR to a promoter DNA enhancing downstream gene expression remains unclear. VraR contains a conserved N-terminal receiver domain (VraR ) connected to a C-terminal DNA binding domain (VraR ) with a flexible linker. Here, we present the crystal structure of VraR alone and in complex with R1-DNA in 1.87- and 2.0-Å resolution, respectively. VraR consisting of four α-helices forms a dimer when interacting with R1-DNA. In the VraR -DNA complex structure, Mg ion is bound to Asp194. Biolayer interferometry experiments revealed that the addition of Mg to VraR enhanced its DNA binding affinity by eightfold. In addition, interpretation of NMR titrations between VraR with R1- and R2-DNA revealed the essential residues that might play a crucial role in interacting with DNA of the vraSR operon. The structural information could help in designing and screening potential therapeutics/inhibitors to deal with antibiotic-resistant S. aureus via targeting VraR.