Based on grey set, grey numbers and their operation properties, the grey numerical model of groundwater seepage system was set up for the first time, the whole grey solving method of the model was given and it was proved that the common solving method of the model was only a special case of the grey solving methods. At the same time, the grey solving method was compared widely with common solving method, classical numerical method. The study shows that the grey solving method is better in depicting the procedure of transporting grey data of groundwater system. On the basis of the theoretical study, two basic kinds of cases about groundwater seepage were selected: the prediction of pit yield and the evaluation of groundwater resources on a groundwater basin. In the cases, systematical analyses were made for generalization and greylization of the hydrogeologic conditions, setting up of the grey model, identification and correction of the model as well as its prediction and evaluation. It was pointed out that when the grey numerical model is used to predict pit yield, the upper limit of the “grey band” of groundwater level cannot be higher than planed safe groundwater level, when evaluating the groundwater resource, the lower limit of the “grey band” of groundwater level cannot be lower than controlled level of groundwater.