A device is provided, which controls a vehicle-mounted engine provided with an engine body with a plurality of cylinders, a plurality of independent intake passages, each connected to the engine body so as to communicate with a combustion chamber of each cylinder via an intake port, and a surge tank connected to an upstream end of each independent intake passage. The device includes a phase changer, an ambient temperature sensor, and a controller configured to acquire an amount of condensate water existing in the surge tank. When the engine is stopped in a situation where the ambient temperature is lower than a given reference temperature and the condensate water amount is above a given reference amount, the controller controls the phase changer so that a lift amount of an intake valve in each cylinder of the stopped engine becomes outside a given minute lift range.