The principle of three heterogeneity characterization methods for hydraulic conductivity, i.e., zoning, Kriging and stochastic modeling were introduced.The paper compared the influence of different methods on results. Taking a contaminated site as an example,the paper comprehensively considered geological formation, data acquiring method and heterogeneity characterization method to design five scenarios.It studied the effects of different scenarios on the groundwater solute transport model,and discussed the advantages and disadvantages of different characterization methods. The results showed that the spatial distribution by Sequential Gaussian Simulation (SGSIM) can reflect the abrupt changes along some boundaries which other methods cannot do. The characterization of hydraulic conductivity using SGSIM provides a better representation of continuous change of conductivity in space than that by the other method. The zoning method gives the largest simulated plume, while the spatial variation of plume is better characterized with SGSIM.The result indicated that stratification, data acquiring method and heterogeneity characterization method should all be taken into consideration to describe the space distribution of permeability coefficient.