In coastal areas, the presence of concrete cracks provides pathways for hazardous ions to ingress from the exterior into the interior of concrete, while the migration of the ions further accelerates concrete deterioration and causes durability problems. The incorporation of graphene oxide (GO) into concrete can inhibit crack initiation and development starting at the nanoscale, improving the concrete microstructure, thereby affecting concrete's resistance to hazardous ion transport and the resulting deterioration. In this study, a multi-scale transport model for cementitious materials with a GO admixture was established to predict the resistance to hazardous ions. Based on the determination of hydration types and hydration kinetics, microstructure modeling was conducted at three scales, the sub-microscale, microscale, and mesoscale, upon which transport property simulations were performed. At the microscale, the effects of both the cement paste matrix and the interfacial transition zone (ITZ) were considered. Through the simulation, it was found that the addition of GO reduced the duration of the induction period and increased the rate of hydration development after the induction period. Moreover, the incorporation of GO could reduce the porosity of cementitious materials at all simulation scales at both early and later ages. At the microscale, it improved the pore structure of the cement matrix and ITZ by reducing large pores and increasing small pores. At all three simulation scales, GO could increase the diffusion tortuosity in hydration products, suppress ion transport, and improve the resistance to hazardous ions of cementitious materials.