This paper presents an intelligent bio-inspired cooperative decoupling control strategy (IBICDC) for the problems of modeling difficulties and strong coupling in the marine boiler-turbine system (MBTS). First, the model of the main steam pressure control loop is successfully constructed by introducing the Martin-Hou equation, which solves the modeling difficulty caused by the complexity of structure, operation mechanism, and operation conditions, as well as the characteristics of nonlinearity, parameter time-varying, and time-delay in the marine boiler (MB). According to the mathematic method of homeomorphic mapping relationship between the rotational speed and the kinetic energy in the marine steam turbine with propeller (MSTP) and the feedback linearization method, the nonlinear degree of the MSTP rotational speed control loop model is reduced and the infinite point of discontinuity in the rotational acceleration when the rotational speed close to 0 is eliminated. Then, the IBICDC inspired by the internal environment regulation mechanism of human body is applied to the strong coupling problem between the two control loops, namely, to eliminate the large value sudden change of the main steam pressure caused by the change of operation conditions. The conventional decoupling methods are also presented. Finally, detailed numerical simulations are conducted to validate the effectiveness of the IBICDC strategy.