In order to provide guidance for water diversion work,it is necessasy to master comprehensively the water quality status and water quality change trend of south-to-north water diversion project area of Jiangsu province.The paper applied the seasonal Kendall method and chose six pollution indices such as DO、CODMn、BOD5、NH3-N、petroleum and volatile phenol from 2001 to 2012 in water route in South-to-north water diversion project area of Jiangsu province to analyze water quality variation tendency of water quality.The results showed that from 2001 to 2012: ①According to type of pollutants, the six water quality indices changed for better. ② According to grade of rivers, the water quality of tributary is good, the water quality of trunk stream except oil index become worse, the other show better trend. ③ According to administrative unit, the water quality is poor because of BOD5 in Yangzhou section, Petroleum in Huaian section , DO and CODMn in Suqian section, the other segment shows better trend.