We address the impact of the relative orientation between donor (D) and acceptor (A) molecules at the D/A heterojunction on the exciton dissociation. For this purpose, two-dimensional heterojunctions of diindenoperylene (DIP) and N,N′-dioctyl-3,4,9,10-perylene tetracarboxylicdiimide (PTCDI-C₈) deposited onto SiO₂/Si are grown, which exemplify two model interfaces with the π-staking direction either perpendicular or parallel to the interface. Aspects related to the morphology of the heterojunctions and charge photogeneration are studied by scanning probe force methods and photoluminescence (PL) spectroscopy. Results from PL spectroscopy indicate that the exciton dissociation is influenced by the different relative molecular orientations of A and D. For the configuration with stronger orbital overlap between A and D at the interface, the exciton dissociation is dominated by recombination from an interfacial charge-transfer state.