Percolation structure is a unified hydrodynamic description of the pore and connected capillary structure of concrete materials. For the concrete which is a system of gel with electrolytic pore solution, both electrical and hydrodynamic parameters were used to describe its percolation structure. Alkali aggregate reaction changes the percolation structure of the concrete. The activity of the alkali active aggregate and the effect of alkali aggregate reaction on the mechanical performance were studied by the change of the percolation structure parameters.