1. A control system for a plant in which a mutual interaction exists between a plurality of control inputs and a plurality of control amounts, comprising: target value-setting means for setting a plurality of target values that are targets of the respective control amounts; and non-interacting input-calculating means for calculating the control inputs as respective non-interacting inputs for causing the control amounts to follow the respective target values, the non-interacting inputs eliminating the mutual interaction, with a predetermined control algorithm based on a plant model formed by modeling the plant into a discrete-time system model, the predetermined control algorithm including a combination of a predetermined response-specifying control algorithm and a predetermined non-interacting control algorithm.