A control method for an internal combustion engine, the internal combustion engine comprising: a variable compression ratio mechanism that varies a mechanical compression ratio of the internal combustion engine; and a variable valve timing mechanism that varies a closing timing of an intake valve, the internal combustion engine having a possibility of combustion instability in a state that the mechanical compression ratio is low and the closing timing of the intake valve is on a retard side, the control method comprising: setting a target compression ratio of the variable compression ratio mechanism and a target control position (tVTC) of the variable valve timing mechanism according to operating condition parameters of the internal combustion engine; judging whether or not an anomaly is present in the variable compression ratio mechanism, wherein the setting includes: when the variable compression ratio mechanism is judged as normal, setting the target control position (tVTC) of the variable valve timing mechanism by using a current value (rVCR) of the mechanical compression ratio as one of the operating condition parameters; and when it is judged that any anomaly is present in the variable compression ratio mechanism, setting the target control position (tVTC) of the variable valve timing mechanism by considering the mechanical compression ratio to be a maximum compression ratio value (VCRmax) achievable by the variable compression ratio mechanism as one of the operating condition parameters; when there is a demand for a reference position leaning operation of controlling the variable valve timing mechanism to a most retarded position and then learning a sensor value of the most retarded position as a reference position, permitting the execution of the reference positon learning operation on the condition that the mechanical compression ratio (aVCR) controlled by the variable compression ratio mechanism is higher than a predetermined compression ratio threshold value (VCRth), wherein the compression ratio threshold value (VCRth) is a value of the mechanical compression ratio at which no combustion instability occurs even when the variable valve timing mechanism is controlled to the most retarded position; and prohibiting the execution of the reference position learning operation when it is judged that any anomaly is present in the variable compression ratio mechanism. setting a target compression ratio of the variable compression ratio mechanism and a target control position (tVTC) of the variable valve timing mechanism according to operating condition parameters of the internal combustion engine; judging whether or not an anomaly is present in the variable compression ratio mechanism, wherein the setting includes: when the variable compression ratio mechanism is judged as normal, setting the target control position (tVTC) of the variable valve timing mechanism by using a current value (rVCR) of the mechanical compression ratio as one of the operating condition parameters; and when it is judged that any anomaly is present in the variable compression ratio mechanism, setting the target control position (tVTC) of the variable valve timing mechanism by considering the mechanical compression ratio to be a maximum compression ratio value (VCRmax) achievable by the variable compression ratio mechanism as one of the operating condition parameters; when there is a demand for a reference position leaning operation of controlling the variable valve timing mechanism to a most retarded position and then learning a sensor value of the most retarded position as a reference position, permitting the execution of the reference positon learning operation on the condition that the mechanical compression ratio (aVCR) controlled by the variable compression ratio mechanism is higher than a predetermined compression ratio threshold value (VCRth), wherein the compression ratio threshold value (VCRth) is a value of the mechanical compression ratio at which no combustion instability occurs even when the variable valve timing mechanism is controlled to the most retarded position; and prohibiting the execution of the reference position learning operation when it is judged that any anomaly is present in the variable compression ratio mechanism.