The aggregation of an amyloid beta peptide (A beta) into fibrils is a key pathological event in Alzheimer's disease (AD). Under certain conditions, Cu2+ markedly inhibits A beta from aggregation and is considered as a potential factor in the normal brain preventing A beta from aggregation. The possible mechanism of the inhibitory effect of Cu2+ was investigated for the first time by molecular dynamics (MD) simulations. On the basis of the radial distribution function analysis of the MD data, a novel strategy, the Q function, was proposed to explore the binding sites of Cu2+ by evaluating the coordination priority of atoms in A beta, and the [6-5-5] tri-ring 4N binding mode of the Cu2+-A beta complexes was found. The mechanism of the conformational transition of A beta from the beta conformation to distorted beta conformations, which destabilizes the aggregation of A beta into fibrils, was also revealed. All the results provide helpful clues for an improved understanding of the role of Cu2+ in the pathogenesis of AD and contribute to the development of an anti-amyloid therapeutic strategy.