Van der Waals (vdW) layered α-In<sub>2</sub>Se<sub>3</sub> 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 In<sub>2</sub>Se<sub>3</sub> 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 In<sub>2</sub>Se<sub>3</sub> phase with the cation sites might being occupied by 1/3 vacancy and 2/3 indium. Our results provide detailed microscopic insights on the phase transition dynamics of the ferroelectric 2H-α In<sub>2</sub>Se<sub>3</sub> in response to the thermal stimulus, and may offer guidelines for the precise controlling of specific In<sub>2</sub>Se<sub>3</sub> phases and the reliability improvement of ferroelectric In<sub>2</sub>Se<sub>3</sub>-based nanodevices.