A control system calculates inputs to a control target that has m inputs and n outputs (m=n, each of m and n is a natural number that is more than one), while designating a plurality of combinations of the inputs and the outputs. A feedback controller calculates, with respect to each designated combination, a control input to a non-interference controller based on a difference between a target value and a current value of the control quantity to make the current value follow the target value. The non-interference controller executes, with respect to each designated combination, a non-interference control to reduce influence due to mutual interference between n control quantities. This reduces the number of combinations of the inputs and the outputs, the combinations whose mutual interference needs considering; thereby, the non-interference control may be easily achieved.