It has been hypothesized that prior to protein domain swapping, unfolding occurs in regions important for the stability of the native monomeric structure, which probably increases the possibility of intermolecular interaction. In order to explore the detailed information of the important unfolding regions in cystatin prior to domain swapping, 20 ns molecular dynamic simulations were performed at atomic level with typical amyloidogenic chicken cystatin (cC) mutant I66Q monomer under conditions that enable forming amyloid fibrils in biological experiments. Our results showed that I66Q mutant exhibited relatively large secondary structure changes and obvious expanding tendency of hydrophobic core compared to wild-type cC. More importantly, the appendant structure (AS) showed a large displacement and distortion towards the hydrophobic core in amyloidogenic cystatin. The structural analysis on cystatin monomer suggested that structural changes of the AS might make the hydrophobic core expand more easily. In addition, analysis on docking dimer has shown that the distorted AS was favor to intermolecular interactions between two cystatin monomers. Data from an independent theoretical derived algorithm as well as biological experiments also support this hypothesis.