An internal combustion engine (1) has a variable compression ratio mechanism (2) that varies a mechanical compression ratio and a variable valve timing mechanism (7) that varies a valve timing of an intake valve (4). When there is a demand to execute reference position learning (step 21) for system calibration of the variable valve timing mechanism (7), the execution of the reference position learning is permitted on the condition that the mechanical compression ratio is higher than a threshold value VCRth (step 22). When any anomaly is present in the variable compression ratio mechanism (2), the reference position learning of the variable valve timing mechanism (7) is prohibited (steps 23 and 25).