A method of and an apparatus for controlling supercharge pressure for a turbocharger in which a proportional control or a proportional plus integral control is selectively carried out for controlling the capacity changing structure of an exhaust gas flow path to a turbine and for controlling an exhaust bypass valve which defines a bypass passage for the exhaust gas to flow around the turbine. Independent control loops are established having electromagnetic valves operated accordance with control signals having duty values calculated by a microprocessor in a control unit. According to the present invention, since independent control loops are established, no interference occurs between the control loops and no overlapping control conditions take place. Also overshoot control for the actual supercharge pressure due to excessive correction according is prevented by utilizing selective control by a proportional or a proportional plus integral scheme.