van der Waals (vdW) layered α-In₂Se₃ possesses stable ferroelectricity even down to monolayer, showing great promise in emerging ferroelectric semiconductor non-volatile memory and in-memory computing. Deciphering the atomistic mechanisms governing its complex phase transition occurring in devices, such as thermal budget during fabrication or cycling, is of critical importance for device performance improvement yet remains challenging due to the intricate polymorphism and low interchange barriers. Here, we directly visualize the unique atomic-level in-plane directional phase transition in 2H-α In₂Se₃ that initiates from the In-Se octahedral framework, and is driven by the migrations of indium ions (in octahedrons) and vacancies (in vdW-gap), revealing a novel intralayer and interlayer indium atoms and vacancies rearrangement pathway. We demonstrate that each In-Se octahedral configuration evolves into two non-layered In-Se tetrahedral frameworks, ultimately coalescing a novel non-layered 6H-type In₂Se₃ phase with the cation sites might be occupied by 1/3 vacancies and 2/3 indium atoms. Our results provide detailed microscopic insights on the phase transition dynamics of the ferroelectric 2H-α In₂Se₃ in response to the thermal stimulus, and may offer guidelines for the precise controlling of specific In₂Se₃ phases and the reliability improvement of ferroelectric In₂Se₃-based nanodevices.