In view of the inharmonious problems between the current situation of water quality and the goal of water function zoning in Xin'an River, the paper first determined the water quality situation and identified pollution contribution matrix of each water quality index by the fuzzy comprehensive assessment on the data of 12monitoring stations in this area. Subsequently, QUAL2Kw model of one dimensional steady water quality was used to simulate the water quality in Xin'an River. Based on the parameters gotten by genetic algorithm calibration, the paper verified the model and then calculated water environmental capacity according to water function zoning. The results showed that QUAL2Kw model can simulate the practical situation of water quality well,but the environmental capacities of total nitrogen in most of the reaches of Xin'an River are negative. The present situation of nitrogen pollution is not optimistic. As to the total phosphorus, though there is a small amount of environmental capacity in water body, but because of the restriction of TP factor, the control of nutrition salt pollution based on environmental capacity need to strengthen.