The geometries of abnormal Watson-Crick hydrogen-bond dimers between cis/trans- O⁶-methylguanine and cis/trans-O⁴-methylthymine and DNA bases (adenine, thymine, cytosine and guanine) have been optimized at the B3LYP/6-311＋G** level. The complete basis-set extrapolation method was employed at the MP2/cc-pVXZ (X＝D, T)//B3LYP/6-311＋G** levels in order to obtain more accurate interaction energies. Counterpoise correction (CP) scheme was also used to take into account of basis set superposition error (BSSE). The all-electron wave functions of these dimers were calculated at the B3LYP/ 6-311＋G** level, and the weak interactions were analyzed by atoms in molecules (AIM) theory. The calculation results show that the methylation of O⁶-guanine and O⁴-thymine can lead to changes of hydrogen-bond interactions between DNA base-pairs, which results in propeller torsions and various displacements between base pairs. The obvious decreases in interaction energies and electron densities between base-pairs is attributed to the methylation on O⁶-guanine and O⁴-thymine. Furthermore, the methylation of O⁶-guanine and O⁴-thymine destabilize the hydrogen-bond interactions of DNA base-pairs, and compared with anti conformations, the destabilization effect of the methylation on cis DNA base-pairs is more evident. Our calculation results are basically in agreement with the experiments.