The intrinsic nature of glass states and glass transitions remain a fundamental open question in condensed-matter physics and materials science. The key to solving the glass transition problem lies in achieving a complete understanding of the physics governing the structural relaxation. Nonetheless, directly probing dynamic atomic-scale structural changes in order to identify the precise local structural motifs and establish quantitative structure-property relationships remains an outstanding challenge. By combining femtosecond electron diffraction with time-dependent density-functional theory molecular dynamics simulations, we directly capture ultrafast amorphous-amorphous transitions indicated by collective bond stretching (0.2 ps) and angle bending (0.5-2 ps) in glassy phase-change material GeTe. The ultrafast bond stretching is accompanied by localized oscillation modes with the frequency of 3.10 THz, unambiguously signaling the local Peierls-like bonding structure and the flexibility of these polarized bonds. These ultrafast collective atomic motions, captured across timescales ranging from femtoseconds to picoseconds, directly reveals the structural origin of the boson peak and provide compelling evidence for many-body interactions in amorphous materials. Furthermore, the ultrafast amorphous-amorphous transitions induce a drastic insulator-metal transition, directly revealing both the underlying switching mechanism and the fundamental speed limit of the ovonic threshold switch. These insights establish a fundamental framework for rationally engineering relaxation pathways and phase-change/threshold switch in amorphous materials. Femtosecond electron diffraction provides a powerful novel approach to deciphering the structural complexity and functional mechanisms of amorphous materials by resolving collective atomic motions from random diffusion dynamics in the time domain.