Circulating cooling water system (CCWS) is an important auxiliary system in the industrial production process, and it is also one of the main energy-consuming units in the whole process. This paper presents a comprehensive operation optimization method of water and energy, and aims to design an optimal operation plan of the CCWS with improved system operation status and reduced system operation cost. To this end, the operation optimization model based on superstructure method is established, which is comprehensive and practical compared with previous researches in two aspects. Firstly, this model is further extended to realize the comprehensive description and synchronous optimization of network structure, equipment operation mode and equipment operation status, and the optimal operation plan of the system is thus obtained. Secondly, the application range of this model is expanded and thus the proposed method is made more general for various of networks. Moreover, proposed optimization model and the solution algorithm are improved with the fusion of domain knowledge. To be specific, the knowledge of system hydraulic balance and system operation are fused into the operation optimization problem, which improves the energy saving optimization effect and the algorithm calculation efficiency. Finally, the practicality of the proposed operation optimization method is verified through simulation experiments based on the actual network data, and the comprehensive energy-saving rate reaches 31.3%, so the system operation costs are effectively reduced. (C) 2018 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.