Molecular beam epitaxy (MBE) of InGaSe/2D[1]GaSe/sapphire hybrid structures has been reported in this study. We explore that MBE of the InGaSe layer on 2D-GaSe/sapphire results in a mixed dimensional alloy, comprising two-dimensional (2D) hexagonal-InxGa1−xSe and three-dimensional (3D) zinc blende (InGa)2Se3, in which the 3D one is more favorable. It is also revealed that the surface morphology of the underneath 2D[1]GaSe layer grown under different modes, i.e., screw-dislocation[1]driven (SDD-GaSe) and layer-by-layer (LBL-GaSe), significantly governs the epitaxial behavior of the InGaSe top layer. Indeed, in the case of the InGaSe alloy grown on 2D LBL-GaSe, it is more and more preferable to nucleate from the edges of GaSe triangular flakes with increasing deposition temperature, thus promoting lateral growth. On the other hand, the surface morphology of InGaSe alloy on 2D SDD-GaSe appears to have a high density of nanoclusters. Moreover, a structural transition from 2D-to-3D has been recognized from in-situ RHEED observation, in which its on-set point is likely accelerated at lower growth temperatures. The gain from this study benefits our understanding of the mixed dimensional GaSe-based heterostructures by MBE, in terms of exploring semiconductor physics and widening potential applications of group-III metal chalcogenides.