Accurate prediction of chloride diffusivity in partially saturated concrete is crucial for durability design of concrete. This study presents an integrated multiscale framework for modelling chloride diffusivity in non-saturated concrete accounting for its microstructural features and 3D moisture distribution. The hierarchical microstructure of concrete at multiscale from nano- to meso-scale is simulated, based on which the fluid-solid interaction and moisture distribution in pore network of concrete with various saturation levels are mimicked using a lattice Boltzmann multiphase model. A lattice Boltzmann-finite difference model for diffusion is developed to simulate the chloride diffusion and predict the chloride diffusivity in non-saturated concrete. Results indicate that chloride diffusivity in partially saturated concrete highly depends on moisture content and distribution, pore structure, and aggregate content. As the water saturation level drops to around 90%, interfacial transition zone starts to retard chloride diffusion. Voids have a great contribution to water saturation level but less effect on chloride diffusivity. The simulated chloride diffusivity at each scale is in good agreement with experimental data.