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In order to develop more effective decoupling control methods for complex coupling system, we present an intelligent bi-cooperative decoupling controller (IBCDC) inspired from the modulation mechanism of internal environment in body. The IBCDC consists of a coordination control unit (CCU), a model identification unit (MIU), a decoupling control evaluation unit (DEU), and two control units. The DEU includes a reinforcing decoupling control block (RDCB) and a suppression decoupling control block (SDCB). Every control unit or block including an original control block (OCB) and a decoupling compensation block (DCB) is designed according to different physiological organs or systems. Under the coordination of the CCU, all the control units or blocks communicate with each other to exchange the control or decoupling control information. Through adjusting the actuators harmoniously, the coupling influences among different control loops can be reduced or almost eliminated. The simulation results demonstrate that the IBCDC can almost eliminate the coupling influence with better control performance. Compared with other decoupling control methods, the IBCDC can be implemented more easily and practically, and be easily generalized to the multiple-input-multiple-output systems.