GMS( Groundwater Modeling System) is an international famous three-dimensional integrated groundwater numerical modeling soft-ware system and characterized by its multivariable modules, all-around functions, wide applycations, intuitional modeling process, friendly op-eration interface etc.This article detailed the general modeling process of GMS applied in the contanminant transport in the groundwater envi-ronment: first, use the MODFLOW module to build the groundwater flow model;second, use the MT3DMS module to build the solute(contan-minant) transport model;finally, use the MODPATH module to build the particle tracking model.Using GMS to simulate and predict the cont-anminant transport in the groundwater is significant for the protection of groundwater and also offers scientifical and technical support and theo-retical foundation for the pollution prevention and controlment.