With the escalating severity of environmental pollution caused by effluent, the wastewater treatment process (WWTP) has gained significant attention. The wastewater treatment efficiency and effluent quality are significantly impacted by effluent scheduling that adjusts the hydraulic retention time. However, the sequential batch and continuous nature of the effluent pose challenges, resulting in complex scheduling models with strong constraints that are difficult to tackle using existing scheduling methods. To optimize maximum completion time and effluent quality simultaneously, this article proposes a restructured set-based discrete particle swarm optimization (RS-DPSO) algorithm to address the WWTP effluent scheduling problem (WWTP-ESP). First, an effective encoding and decoding method is designed to effectively map solutions to feasible schedules using temporal and spatial information. Second, a restructured set-based discrete particle swarm algorithm is introduced to enhance the searching ability in discrete solution space via restructuring the solution set. Third, a constraint handling strategy based on violation degree ranking is designed to reduce the waste of computational resources. Fourth, a Sobel filter based local search is proposed to guide particle search direction to enhance search efficiency ability. The RS-DPSO provides a novel method for solving WWTP-ESP problems with complex discrete solution space. The comparative experiments indicate that the novel designs are effective and the proposed algorithm has superior performance over existing algorithms in solving the WWTP-ESP.