Optimal control system has been considered as a valuable technique to enhance the reliability and security of wastewater treatment process (WWTP). However, due to the complex environments, it is difficult to realize the optimal control with changeable operational conditions in WWTP. To overcome this problem, an intelligent optimal control system with flexible objective functions (IOCS-FOF) was proposed in this paper. The main merits of this proposed IOCS-FOF were shown as follows. First, an optimal control system scheme was developed, where different time-scale operational objectives were detailed to describe the operational features. Second, a flexible objective strategy was designed to determine suitable objective functions, which could adapt to complex environments of WWTP. Third, a novel dynamic multiobjective optimization algorithm for flexible objectives (FO-DMOA) was developed to obtain the optimal solutions of IOCS-FOF. Finally, the proposed IOCS-FOF was applied in the benchmark simulation model No. 1 (BSM1) to confirm its technique capability. The results demonstrate that this proposed method can improve the operation performance of WWTP.