Fourier transform infrared spectroscopy with multiple internal reflection mode (FTIR-MIR) has been applied for the first time to measure the permeability of concrete. The effect of water-cement ratio and curing time on the microstructure and permeability of concrete was studied. Also, the penetration process of H2O and SO2-4 through the concrete specimens was investigated. The results indicated that the movement of H2O through unsaturated concrete was mainly caused by capillary suction and the movement of SO2-4 through unsaturated concrete should take into account diffusion, advection caused by a capillary suction flow and the reaction between SO2-4 and the cement hydration products. The permeability of concrete was determined by its microstructure. With the decrease in water-cement ratio and the increase in curing time, the porosity and the connectivity of pores in concrete decreased, which resulted in the decrease of concrete permeability.