Abstract Understanding the evolution mechanisms of interlayer stacking structures, particularly at the atomic scale, is of great significance for modulating the physical properties and realizing the full potential of 2D materials in electronics and quantum information applications. Herein, by performing in situ experiments using aberration corrected scanning transmission electron microscopy, the evolution of diverse interlayer stacking sequences (from 3R to N, N to 3R and N(3R) to AB′-stacked) in bilayer PtSe₂ are directly observed. Furthermore, the interlayer rotational angles are tuned (e.g. 13.3° to 9.4°, 16.8° to 11° and 16.1° to 6°) in situ at real time in bilayer PtSe₂. Density functional theory calculations reveal a small energy barrier (<0.2 eV per formula unit) for the kinetic evolution of interlayer structures. The illumination electron beam, while being as an atomic-scale probe for imaging, transfers enough energy initiating the transition. The bilayer PtSe₂ has show the rich stacking and twisted structures which may create novel physical phenomena. These findings shed new light on the diversity of structural properties of bilayer PtSe₂, which may be valuable for constituting a step further toward their potential uses for next generation of 2D transition metal dichalcogenides-based device applications.