One of pathological features of Alzheimer's disease (AD) is extracelluar aggregation of amyloid-β protein (Aβ) forming senile plaques. Investigation on inhibition of Aβ aggregation can be crucial for designing effective drugs against AD. Previous studies have demonstrated that the deamidation at Asn27, a type of post translation modification, significantly prevented the polymerization of Aβ monomers. But the underlying mechanism is still unclear. Therefore, we investigated the possible effect of Asn27 deamidation on structure and aggregation of Aβ42 monomer using molecular dynamics simulation. The results showed that the deamidation of Asn27 can directly disrupt the salt bridge formed between D23 and K28, and effectively decrease the content of β-sheet that is important for aggregation of Aβ. Moreover, the inability at C-terminal region (CTR) and N-terminal region (NTR) to form antiparallel β-sheets further weakens the intra-peptide interaction of Aβ42 monomer. These changes caused by Asn27 deamidation lead to the decline of the aggregated trend of Aβ42 monomer, which is consistent with the experimental observation. According to these results, the salt bridge formed between D23 and K28 plays an important role in promoting the polymerization process between Aβ42 monomers, and disrupting this interaction may be a potential direction for further designing drugs to inhibit aggregation of Aβ42. In summary, this study shows a potential affected site that can efficiently inhibit aggregation of Aβ42.