In this study, metakaolin (MK)–ground granulated blast furnace slag (GGBFS) was used to prepare geopolymer mortar, and concrete was prepared using prismatic-shaped basalt or aged cement mortar block as coarse aggregate. The pore structure characterization of the mortar, chloride binding capacity of the corresponding paste and the micro dimension of the interfacial transition zone (ITZ) in concrete were analysed by using a mercury intrusion porosimeter, the chloride adsorption equilibrium method and scanning electron microscopy-energy dispersive spectroscopy, respectively. The medium transmission properties of the concrete and corresponding mortar were analysed through a moisture diffusion test, chloride migration test, and chloride natural diffusion test. On this basis, the permeability resistance of the ITZ in geopolymer concrete was studied by manipulating the parameters for the basalt aggregate. The result shows that the geopolymer mortar exhibits higher porosity compared to cement mortar with similar strength, while the most probable pore size is significantly smaller, with more than 80% of the pores showing a pore size of less than 50 nm. The chloride binding mechanism for geopolymer paste primarily involves physical adsorption, and shows a greater binding capacity than cement paste at a chloride ion concentration greater than 1 mol/L. The medium transmission coefficient for geopolymer concrete is found to be 55.1–79.0% of that of cement concrete for the same parameters of the coarse aggregate. The impermeability of geopolymer concrete and its ITZ is found to be always better than that of cement concrete for varying parameters of the coarse aggregate.