We study the quantum dissipative dynamics of charge transfer excitons localizing and dissociating at the interface of a molecular heterojunction typical for organic photovoltaics. The excitons dynamics can be separated into a short-time regime with short-lived electronic coherence and a long-time regime with a slowly decaying incoherent dynamics. On the short time scale (<300 femtoseconds), the excitons are coherently delocalized along the molecular chain. On a long time scale (few picoseconds), charges get localized and relax to the lowest-energy charge transfer state. However, the long-time dynamics still involves excitons which are delocalized along the chain. This is favored by the strong coherent mixing of states on the charge transfer manifold. Furthermore, molecular vibrations dramatically hamper electron-hole separation. Our work thus may motivate the design of new materials with a more rigid molecular backbone.