The land cover change and the non-point source pollution output risk in Nansihu Lake Basin during 1990-2015 were analyzed based on the land use data and statistical data. The method of output risk model, CA-Markov model and Regression Model were used, and combined with GIS technology, the land use pattern and the export risk distribution in 2020 were simulated. The results were as follows. In the 25 years, farmland and arable land were the main land use types in the study area, accounting for more than 85% of the total area. The TN and the TP risk changes were significantly different. The TN output risk value ranged between 0-0.65, and the TP output risk value was 0-0.12. N was the main pollutant. The TN risk increased gradually from 1990 to 2005, decreased significantly during 2005-2005, and increased sharply during 2010-2015. The TP risk decreased gradually during the 25 years. The low risk areas were mainly distributed in the eastern part of Nansihu Lake basin, while the high risk areas were mainly in the west part of the lake basin. The land use change in 2020 was predicted. Compared with 2015, the arable land is increasing, the area of unused land is unchanged, and the other types are reducing to different degrees. The TN risk is reducing slightly. TP risk is unchanged. It is necessary for the local government to focus on improving the agricultural science and technology and reducing fertilizer use so as to control the status quo of non-point source pollution in Nansihu Lake Basin.