As the main force of scientific and technological innovation in the development of water conservancy, the research institutions of water conservancy need to build a complete and effective performance evaluation system for fair and scientific performance evaluation in order to implement the requirements of the national science and technology innovation management mechanism of China. A performance evaluation system is established based on the requirements of the national science and technology innovation management mechanism and the characteristics of scientific research institutions of water conservancy in the new era. The weight of each index is determined through the analytic hierarchy process, and the triangular whitening weight function in the gray clustering method is used to evaluate the performance of scientific research institutions. Taking Water Conservancy Science Institution in J Province as an example for empirical analysis, the evaluated results of performance is good, and the related suggestions are put forward to provide a basis for strengthening internal and external management and improving the index system for the performance of research institutions of water conservancy.