In evaluations of river health, in order to overcome the defects of the traditional grey clustering method，the method of common origin clustering was introduced to improve the set pair model, the efficacy function was used to replace the link component to play the advantages of the common origin clustering method, i.e., wide coverage, and to use the set pair model to deal with the uncertainty information. At the same time, the combination weighting method, which combined both the subjective and objective weighting methods, was used to determine the weights of the indexes, then a set pair analysis model based on the common origin cluster was constructed and applied to the river health assessment. According to the evaluation results, the overall health of the river was good, but we should focus on improving the amount of water supply, protecting the ecological diversity and improving the river quality.