Abstract A two-dimensional epitaxial growth template for organic semiconductors was developed using a new method for transferring clean graphene sheets onto a substrate with controlled surface wettability. The introduction of a sacrificial graphene layer between a patterned polymeric supporting layer and a monolayer graphene sheet enabled the crack-free and residue-free transfer of free-standing monolayer graphene onto arbitrary substrates. The clean graphene template clearly induced the quasi-epitaxial growth of crystalline organic semiconductors with lying-down molecular orientation while maintaining the “wetting transparency”, which allowed the transmission of the interaction between organic molecules and the underlying substrate. Consequently, the growth mode and corresponding morphology of the organic semiconductors on graphene templates exhibited distinctive dependence on the substrate hydrophobicity with clear transition from lateral to vertical growth mode on hydrophilic substrates, which originated from the high surface energy of the exposed crystallographic planes of the organic semiconductors on graphene. The optical properties of the pentacene layer, especially the diffusion of the exciton, also showed a strong dependency on the corresponding morphological evolution. Furthermore, the effect of pentacene–substrate interaction was systematically investigated by gradually increasing the number of graphene layers. These results suggested that the combination of a clean graphene surface and a suitable underlying substrate could serve as an atomically thin growth template to engineer the interaction between organic molecules and aromatic graphene network, thereby paving the way for effectively and conveniently tuning the semiconductor layer morphologies in devices prepared using graphene.