The mechanism of the clustering in Al-Mg-Si-Cu alloys has been a long-standing controversial issue. Here, for the first time, the mechanism of the clustering in the alloy was investigated by a Kinetic Monte Carlo (KMC) approach. In addition, reversion aging (RA) was carried out to evaluate the simulation results. The results showed that many small-size clusters formed rapidly in the early stages of aging. With the prolongation of aging time, the clusters merged and grew. The small clusters formed at the beginning of aging in Al-Mg-Si-Cu alloy were caused by initial vacancies (quenching vacancies). The merging and decomposition of the clusters were mainly caused by the capturing of vacancies, and the clusters had a probability to decompose before reaching a stable size. After repeated merging and decomposition, the clusters reach stability. During RA, the complex interaction between the cluster merging and decomposition leaded to the partial irregular change of the hardness reduction and activation energy.