The supercharger pressure control system includes a sensor for detecting the supercharger pressure of the engine and regulates the pressure through a variable geometry device or an exhaust bypass valve. The control for the pressure regulation is carried out by comparing the sensed supercharge pressure with a target value. Any difference determined by this comparison is accumulated by a computer as an error and a basic control value is determined based on the error. Alternatively, a predetermined basic control value for the engine intake air is corrected in accordance with the error and this control value or corrected value is used to control the operation of the supercharge pressure regulator. This causes the regulator to operate in a manner responsive to variations in performance of the engine or turbocharger, thus maintaining the supercharged pressure within a permissible range of a target value.