Density functional theory (DFT) calculations were performed at the B3LYP/6-311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li+, Na+, K+, Be2+, Mg2+, and Ca2+ (Mn+, hereinafter), with nucleobases, namely, adenine, cytosine, guanine, thymine, and uracil. Morokuma decomposition and orbital analysis were used to analyze the binding components. A total of 150 initial structures were designed and optimized, of which 93 optimized structures were found, which could be divided into two different types: cation-pi complex and cation-heteroatom complex. In the former, a Mn+ is located above the nucleobase ring, while in the latter a Mn+ directly interacts in flank with the heteroatom(s) of a nucleobase. The strongest binding of -319.2 kcal/mol was found in the Be2+-guanine complex. Furthermore, the planar ring structures of the nucleobases in some cation-pi complexes were deformed, destroying more or less the aromaticity of the corresponding nucleobases. In the cation-heteroatom complex, bidentate binding is generally stronger than unidentate binding, and of which the bidentate binding with five-membered ring structure has the strongest interaction. Moreover, the calculated Mulliken charges showed that the transferred charge is linearly proportional to the binding strength. Molecular orbital coefficient analysis indicated a significant orbital interaction in cation-pi complex, but Dot in cation-heteroatom interaction. In addition, Morokuma decomposition revealed that electrostatic interaction is more important for cation-heteroatom binding. The majority of the calculated DeltaH values are in good agreement with the experimental results. In those cases with significant differences, the experimental results are proximate to an average of the DeltaH values of two isomers formed by the same nucleobase and cation.