The nonadditivity of stacking interactions in stacked structures of adenine–thymine and guanine–cytosine base pairs is investigated by MP2 and SCS-MP2 calculations with 6-311++G** and aug-cc-pvdz basis sets. The calculation results indicate that the intermolecular distances in the multi-stacked structures do not become shorter obviously as the stacked structure added. The middle stacking interaction energies in the multi-stacked structures also become weaker than that of dimer structures. It is found that the total stacking interaction energies of the trimer and tetramer stacked structures do not increase proportionally. Based on the results, we suggest that there is negative cooperativity of the stacking interactions in the adenine–thymine and guanine–cytosine stacked structures.