In an engine provided with a valve lift amount variable mechanism and a center phase variable mechanism for an intake valve, a region between a region where a flow rate of an intake air passing through the intake valve reaches a sonic speed and a region where an intake air amount does not substantially change relative to a change in an opening area of the intake valve is made to be a learning region. Then, in order to resolve an error in intake air amount in the learning region, a correction value for correcting control process of the valve lift amount variable mechanism is learned. When the learning of the correction value is converged, the learning correction value is corrected with an occupied rate of the valve lift amount variable mechanism in the influence ratio between influences on the two mechanisms in relation to the error. Further, based on the error occurring in a state corrected with the learning correction value which is corrected with the influence ratio, a correction value for correcting control process of the center phase variable mechanism is learned.