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Hydraulic transients may pose a critical threat to process operation due to devastating surge waves. This paper investigates hydraulic surge and damping control associated with pipe flow modeling and valve optimization. A one-dimensional transient model was developed using the modified instantaneous accelerations-based (IAB) model, considering energy dissipation, referred to as the compression–expansion effect, which was then solved by the Method of Characteristics (MOC). Analogous to solving valve operation by means of the traveling salesman problem (TSP), a novel surge damping strategy was proposed by applying an improved artificial fish swarm algorithm (AFSA). After validating the unsteady model and the optimization algorithm, wave surge damping effectiveness was evaluated on the basis of case studies in different pump running scenarios. The results showed that the proposed nonlinear optimized control method was able to reduce surge amplitude by 9.3% and 11.4% in pipe systems with and without running centrifugal pump, respectively, and was able to achieve a 34% time margin or a maximal 75.2% surge reduction in the case of using an positive displacement pump. The optimized nonlinear valve closure presents different shapes in fast closing and slow closing situations. The strategy proposed in the present study is beneficial for guiding valve real-time control, as well as providing a reference for valve design for the purpose of wave surge protection.