On the basis of summarizing the applications of financial accounting methods of watershed ecological compensation to some provinces and cities in China, this paper introduces the financial accounting method of watershed ecological compensation in Jiangsu Province in 2014. The ecological compensation fund of each city in Jiangsu Province is accounted according to the measured water quality data in the year of 2013, and the existing problems are analyzed. The current method of calculating ecological compensation funds, which is based on the water quality comprehensive over-standard times, does not take into account the river flow. To solve this problem, a method of calculating the expenses of contaminant treatment in sewage treatment plants is put forward based on the over-standard flux. The method was used to calculate the ecological compensation fund of each city in Jiangsu Province in 2013. The calculation results show that this method can be used to optimize the current financial accounting method of watershed ecological compensation.