A method and apparatus is disclosed to control the operation of an air charging system of an internal combustion engine. A plurality of output parameters of the air charging system are monitored. An error is calculated between the monitored output parameters and a target value thereof. The calculated errors are applied to a linear controller that yields a virtual input used to calculate a plurality of input parameters for the air charging system. The input parameters is used to determine the position of a corresponding actuator of the air charging system for operating the actuators according to the determined position thereof. The inputs parameters are calculated with a non-linear mathematical model of the air charging system configured such that the virtual inputs are in a linear relation with only one of the output parameters and vice versa.