A system and method of controlling an internal combustion engine are provided. The method may include closing said intake valve at a timing in a first range, which is before a maximum charge closing timing with which an amount of air inducted into said cylinder from said air intake passage would be maximized at a given engine speed, during a cylinder cycle when a desired amount of air to be inducted into said cylinder is less than or equal to a predetermined air amount at the given engine speed. The method may further include closing said intake valve at a timing in a second range, which is after said maximum charge closing timing and separated from said first range during a cylinder cycle, when a desired amount of air to be inducted into said cylinder is greater than said predetermined air amount at the given engine speed.