A model of phosphorus purification in a watershed was established based on the export coefficient and purification index of phosphorus in different types of land cover. The model was employed to simulate the economic value of the ecosystem service with the expected water quality standard and marginal cost of pollutant purification of the upper reaches of Xin’an River of Anhui, China. The results revealed that from 2000 to 2010, some farmland outside the Tunxi, Jixi, Shexian, Yixian and Xiuning was converted to builtup land. The total amount of phosphorus exported to the upper Xin’an River decreased a little, and the main source of phosphorus pollution was farmland and builtup land. More than half of the exported phosphorus was efficiently purified by different types of land cover via flow accumulation. The pattern of purification and export of highly concentrated phosphorus showed the same trend which occurred in the northern part of the watershed including the Yangzhi River, Fengle River and Hengjiang River. Forestland and grassland did not efficiently purify phosphorus in the watershed owing to the irrational distribution of existing land cover. The total service value was 3.80 and 3.31 million Yuan in 2000 and 2010, respectively.