Abstract: In this paper,The flux difference splitting(FDS) scheme is applied to two-dimension flow-pollutant numerical simulation.Some simplified models in ideal conditions are used to analyze the accuracy of FDS scheme.The model of steady point source discharge shows high accuracy.To reduce numerical diffusion in big concentration grades,a limited flux is added to the first order scheme so as to derive the second order scheme.The results of water quality discontinuities model prove that FDS second order scheme can catch discontinuities with so high resolution that it can accurately simulate big concentration grades or abrupt water quality jump.The successful application in water environment numerical simulation of Nantong section of Yangtze River ulteriorly validates the practical application ability of FDS scheme.