Circulating cooling water systems are a kind of commonly used industrial auxiliary systems with great energy saving potential, but the energy-saving retrofit of the system is often blindfold. Therefore, this paper performs an analysis and research on energy-saving retrofit of a circulating cooling water system based on energy-saving bottleneck diagnosis to improve the targeted and energy-saving effects. According to the system characteristics, the energy decomposition method is improved, and the multi-case energy efficiency decomposition method is proposed. Combining this method with the orthogonal test analysis method, this paper designs a two-dimensional energy-saving bottleneck diagnosis method. Then the system energy-saving status is analyzed, and the retrofit priority of each system part is determined. Based on the retrofit priority, combined with the corresponding retrofit measures, the optimization problem is formed to realize the design of the retrofit scheme. In addition, combined with post-project evaluation knowledge, each optimal scheme is evaluated to provide decision makers with more decision information. Finally, through a case application, the effect of this method is verified.