Chao Lake is one of the five largest fresh lake in China and important to the socio-economy development of Anhui Province. With the enforcement of agricultural development, agriculture planting and stock breeding sectors boosted quickly and None Point Source(NPS) Pollution has become a considerable source contributing to the total pollutants loads into Chao lake. It is essential to study NPS pollutants loading amounts and their spatial distribution for taking effective countermeasures to control NPS pollution. It is a complex task to estimate the contribution of different NPS sources in a large watershed like Chao lake. When there is no extensive pollutant discharge monitoring data, no adequate soil, land use, atmospheric and hydrodynamic data, Export Coefficient Methods (ECM) could be more practical for evaluating NPS pollution and its spatial distribution in large scale watershed. In this paper, ECM was applied using county level statistical datasets(for the year 1990, 2000 and 2009) in Chao lake watershed to assess NPS pollutants loading and their spatial distribution. The research results showed that: The research showed that: i) Total Nitrogen (TN) and Total Phosphorus(TP) generated in Chao lake watershed were 36979, 65042, 77706 and 8973, 23560, 30383 tons respectively for the year 1990, 2000 and 2009, which kept increasing trend for the past three decades; ii) For the year 2009, Livestock/Poultry Breeding sector contributed 73.8% of the TN generation, which followed by domestic waste water(15.2%) and fertilizer using(10.9%). however, Livestock/Poultry Breeding sector contributed 91.7% of the TP generation; iii) The top three counties were Feixi, Feidong and Wuwei, whose amounts of TN and TP generation accounted for 57% and 60% of the whole Chao lake watershed. Therefore effective countermeasures should be taken to control the generation and discharge amount of TP to improve water quality of Chao Lake.