The morphology of MoS2 nanostructures was manipulated from thin films to vertically aligned few-layer nanosheets on graphene, in a controllable and practical manner, using metalorganic chemical vapor deposition. The effects of graphene layer and MoS2 morphology on photoelectrochemical (PEC) performance were systematically studied on the basis of electronic structure and transitions, carrier dynamic behavior, and PEC measurements. The heterojunction quality of the graphene/vertical few-layer MoS2 nanosheets was ensured by low-temperature growth at 250−300 °C, resulting in significantly improved charge transfer properties. As a result, the PEC photocurrent density and photoconversion efficiency of the few-layer MoS2 nanosheets significantly increased upon the insertion of a graphene layer. Among the graphene/MoS2 samples, the few-layer MoS2 nanosheet samples exhibited shorter carrier lifetimes and smaller charge transfer resistances than the thin film samples, suggesting that vertically aligned nanosheets provide highly conductive edges as an efficient pathway for photo-generated carriers and have better electronic contact with graphene. In addition, the height of vertical MoS2 nanosheets on graphene should be controlled within the carrier diffusion length (~200 nm) to achieve the optimal PEC performance. These results can be utilized effectively to exploit the full potential of two-dimensional MoS2 for various PEC applications.