Phase-change materials are promising foundations for both nonvolatile storage and neuro-inspired computing applications. An attractive phase change material K2Bi8Se13 (KBS) was recently discovered to possess fast structural transition and outstanding property contrast, yet the underlying mechanism remains unclear. We conducted ab initio molecular dynamics simulations to investigate the transition of KBS from a crystalline to amorphous phase. Initiated by the Bi–Se bond breaking at the boundaries of atom blocks, the simulated phase transition proceeds through the conversion between BiSex octahedral and pyramid structures. Remarkable discrepancies in electronic structures and absorption spectra between the two phases are further illustrated by density functional theory simulations, which reproduce the experimental observations. The optical and electrical contrasts between the two phases are found to originate from the band edge states localized at various atom blocks that uniquely appear in the crystalline phase. These states provide pseudo one-dimensional transport channels with resonant bonding that may further intensify the electrical contrast. The distinct phase change properties compared with traditional phase change materials can be attributed to the hierarchical KBS crystal structure comprised of loosely bound atom blocks. The above findings pave an avenue toward the design of phase change materials beyond the traditional scope of the Ge–Sb–Te triangle map.