Characterizing and controlling the interlayer orientations and stacking orders of two-dimensional (2D) bilayer crystals and van der Waals (vdW) heterostructures is crucial to optimize their electrical and optoelectronic properties. The four polymorphs of layered gallium selenide (GaSe) crystals that result from different layer stackings provide an ideal platform to study the stacking configurations in 2D bilayer crystals. Through a controllable vapor-phase deposition method, bilayer GaSe crystals were selectively grown and their two preferred 0° or 60° interlayer rotations were investigated. The commensurate stacking configurations (AA' and AB stacking) in as-grown bilayer GaSe crystals are clearly observed at the atomic scale, and the Ga-terminated edge structure was identified using scanning transmission electron microscopy. Theoretical analysis reveals that the energies of the interlayer coupling are responsible for the preferred orientations among the bilayer GaSe crystals.