In order to quantitatively assess the present situation of rivers, to maintain river ecological environment, to improve the sustainable management of river, and to establish river health assessment system, the entropy value method was introduced into mutation model for coupling. To avoid the errors caused by the subjective weight assignment of evaluation index in traditional evaluation method, and to apply the model to the Qinhuai river health assessment, step by step evaluation was conducted from four layers, finally it was concluded that the health comprehensive index of the Qinhuai river was 0.97, being in good condition. This showed that, at the present stage, the basic components of Qinhuai river system were generally complete, but the water quality problem was outstanding, which was the main factor that controlling river health. Therefore, it is neccessary to control pollution in order to strengthen ecological protection.