Abstract: Numerical simulation is a primary method for studying the flow and transport in porous media.It is rather important to specify the exact value of parameters,which can represent the real hydraulic feature during the numerical simulation of groundwater.As the porous media is a complex system,particularly when the studyied area is large-scale,the spatial variability of hydraulic parameters is especially significant.The traditional deterministic model has certain limitation in considering the spatial variability.This study performs the numerical simulation via the Monte Carlo method,which can take such spatial variability into account to study how the spatial variability effects the numerical simulation.The monte Carlo simulation of flow and transport is used to compare with the deterministic model in three-dimensional heterogeneous media.And a series of comparisons,such as the difference in hydraulic head,velocity and tracer concentration,show that the Monte Carlo simulation is more effective because it has a higher resolution and a good explanation to the simulation error and the source of such error.