The numerical simulation of the contaminant transport in subsurface porous media have been a hotspot for years. It is always considered to be tough to deal with the problems regarding the numerical dispersion and the oscillation around sharp front area of contaminants. This paper presents a new method which can reduce the numerical dispersion in the numerical modeling of the contaminant transport in groundwater. The core of the new method is adding a new numerical dispersion estimation term to the hydrodynamic dispersion coefficient and obtaining a modified hydrodynamic dispersion coefficient (MHDC). We use MHDC instead of the traditional hydrodynamic dispersion coefficient and put forward a new parameter of numerical dispersion factor (μNDF). The research area can be divided into different μNDF areas, and their values can be adjusted according to our needs. In this way, we can control the numerical oscillation and diminishing the numerical dispersion. The Simulated results of several examples from one-dimension problems to two-dimension problem indicate that the new method can considerably reduce the numerical dispersion on the basis of diminishing the numerical oscillation and obtain more precise simulation results. Hence, the new method is simple in theory, convenient in application and worth popularizing.