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.