Soil core is commonly used in seepage flow test of centrifuge test, in which soil samples do not scale with the same rate as the model so that the fluidflow doesn’t follow the similarity criterion of hydrodynamic. Based on the similarity criterion of hydrodynamic and centrifuge test, it was proposed to achieve good similarity with adjustment of particle diameters and hydro material parameters. As it was difficult to adjust particle diameters and hydro material parameters, and based on the characteristics of distinct element method (DEM), particle flow code (PFC) was adapted to simulate seepage deformation in centrifuge test. It was indicated that the seepage flow field of the model was in good consistent with that of soil core which approved by theory analysis and experimental test. And it was shown that PFC can be practicably used in studying centrifuge test and provide reference to use PFC in centrifuge test involved seepage flow.