The study area was designed and constructed, based on the simplification of a conceptual model, to develop a three-dimensional groundwater flow model for simulation of two-layers system. Finite difference groundwater flow model was constructed for the Central Songhuajiang River alluvial plain in Northeast China, with the coverage of 786.6km2.The grid networks with a spacing of 474.4m by 509.5m were used to cover the model area. The trial-and-error technique was used to calibrate the model. The sensitivity of the simulations to the model parameters was studied and the most sensitive parameters that controlling the residual heads distribution in the Songhuajiang River valley were defined.