A method of controlling the operation of an air charging system is disclosed. A plurality of output parameters of the air charging system are monitored. An error between each one of the monitored output parameters and a target value thereof is calculated. Each one of the calculated errors is applied to a linear controller that yields a virtual input which is used to calculate a plurality of input parameters for the air charging system. Each one of the input parameters is used to determine the position of a corresponding actuator of the air charging system and operate of 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 each one of the virtual inputs is in a linear relation with only one of the output parameters.