Abstract: A 3-D flow and matter transport numerical model is budded in the improved σ-coordinate system in this paper.A vertical transform coefficient is used in this work.The govern equations,the boundary conditions and the initialization condidons are obtained through the strict calculation.The rmdel is dispersed by finite difference method (FDM).The computation program is expressed wrath Fortran.The model and its program are confirmed by the test computation of the flow and the salinity process in part sea area of the Oujiang estuary.