In a method for controlling an engine, based on a control map of an engine speed N and a fuel injection amount Q of a common-rail fuel injection unit, a controller calculating the fuel injection amount Q depending on the engine speed N, calculating an injection amount deviation ΔQn as a fuel injection amount increase, and determining that an engine is in a transient state if the injection amount deviation ΔQn exceeds a reference transient injection amount deviation A2 or if a transient injection amount deviation count Xq is larger than or equal to a reference transient injection amount deviation count X2. If it is determined that the engine is in the transient state, the controller controls an EGR unit and a boost controller according to an excess air ratio λ that is an indicator indicating the state of the engine.