Based on the advantage of variogram that can indicate the characteristic of aperture for relativity and randomicity of space change, Kriging is used to estimate aperture of single fissure. It is shown that the result is reasonable through cross validation. The experiment of solute transport on single fissure shows that it is reliable using Kriging to estimate of aperture for single fissure. So it is feasible for the means of stochastic simulation to compute aperture.