In this paper, the classical molecular dynamics method is used to investigate the permeability of pressure-driven water fluid in the hybrid structure of graphene-carbon nanotube (CNT). The results indicate that the permeability of water molecules for the hybrid structure of graphene-CNT is obviously higher than that for the assembled structure of graphene-CNT. The combination between the graphene sheet and CNT in the hybrid structure is found to be a key point to improve the permeability of water molecules. Subsequently, the potential of mean force (PMF) is calculated in order to explain the influences of the combined structure on the permeabilities for the water fluid passing through both the hybrid and assembled graphene-CNT structures. The result shows that the PMF for the water molecules penetrating through the assembled structure is larger than that for the hybrid structure appreciably. It implies that the structure of the combined chemical bonds in the hybrid structure can efficiently improve the permeability of water molecules. As for the water penetrating through the hybrid structured graphene-CNT, the permeability of water increases with water pressure rising, and decreases with the electric field intensity increasing. The water molecules cannot pass through the proposed hybrid structure below a pressure threshold of 100 MPa. The permeability of water in the hybrid structure decreases with the increasing charge quantity on CNT below a threshold of 0.8e. The PMF for water penetrating through the hybrid structure decreases with charge quantity decreasing. The results suggest that the water permeability can be controlled by regulating the water pressure and the electric field intensity. Furthermore, the influences of the temperature and the axis spacing of two CNTs in the hybrid structure on the water permeability are considered. The permeability of water in the hybrid structure increases with the increasing temperature above a threshold of 200 K. The PMF for water penetrating through the hybrid structure increases with the decreasing temperature. Interestingly, the water permeability decreases with the increasing axis spacing. As the axial spacing increases, the water permeability decreases gradually and even approaches to two times of the permeability in the case of the hybrid structure with a single CNT channel. The findings can provide a theoretical basis for designing nanopumps or osmotic membranes based on the graphene-CNT hybrid structures.