The linkage of Generalized Watershed Loading Functions model(GWLF) and one dimensional water quality model( QUAL2Kw) was applied in the main stream of Xin'an River located in Huangshan segment so as to realize the water quality model to apply in the river segment of a non-point oriented watershed. The paper took the result of non-point source load as the input data of GWLF model, and combined the release records of point source to carry out water quality simulation. The results indicated that through the linkage of GWLF and QUAL2Kw model, QUAL2Kw model can better simulate the status of the river water quality. The proportion of non-point source pollution contribution to each pollutants of Jiekou section is notable. The proportions of each pollutants are CBOD（31.78%）, total nitrogen (45.85%), ammonia nitrogen （23.11%）and nitrate nitrogen 70.86%）. Such contribution apportionments to Jiekou section could be used by local water quality management agency to adopt specific pollution reduction measures so as to achieve effective protection of water environment.