An engine control system comprises a NOx catalyst selectively reducing NOx from exhaust gases, a reducing agent supply providing the reducing agent to an exhaust system and positioned upstream of the NOx catalyst, NOx sensors detecting an amount of NOx in exhaust gases emitted by an internal combustion engine, a fuel injection system injecting fuel to the internal combustion engine in a main injection mode or a pilot-and-main injection mode, and a control unit activating the fuel injection system in the pilot-and-main injection mode when a NOx purifying efficiency determined on the basis of data of emitted NOx is equal to or below a preset purifying efficiency.