A method for controlling an engine which comprises a combustion pressure sensor includes receiving a combustion pressure signal from the combustion pressure sensor. An Indicated mean effective pressure (IMEP) deviation for each cylinder and an IMEP deviation for each driving cycle for the engine are calculated based on a combustion pressure according to the received combustion pressure signal. A main injection timing is set based on a difference between the calculated IMEP deviations for the each cylinder and a difference between the calculated IMEP deviations for the each driving cycle. The engine runs by injecting a fuel according to the set main injection timing.