A method of controlling an engine system equipped with a supercharger may include determining a target value of boost pressure, depending on an rpm of an engine and then determining whether the supercharger is in an operable region, deducing a target rpm of the supercharger, based on a reference value previously input into the controller and a current state value of a vehicle input into the controller, when it has been determined in the operating-region determination that the supercharger is in the operable region, setting a maximum value, in the target rpm deduced in the target-rpm deduction, to a drive rpm of the supercharger, and verifying whether the set drive rpm is greater than or equal to a predetermined reference value previously input into the controller, and driving the supercharger at the set drive rpm, by closing the bypass valve to open the supercharger path.