An apparatus for controlling an engine and a method thereof are provided. The apparatus includes an integrated thermal management (ITM) that adjusts opening of a plurality of valves as a cam rotates and a storage that stores a table for differential pressure between a front end and a rear end of each of the plurality of valves, based on an engine revolution per minute (RPM) and an ITM angle. A controller determines a state of the ITM and adjusts opening degrees of the plurality of valves depending on the differential pressure of the valve, based on the differential pressure table based on the state of the ITM.