A control system for fuel injection by predicting engine noise may include an engine noise predicting device configured to derive a predicted engine noise value in real time by a predicted engine noise coefficient which is pre-stored according to a currently measured combustion pressure value of an engine; and a combustion controller configured to determine a difference between the real-time predicted engine noise value derived by the engine noise predicting device and a target engine noise value for a current operation condition of the engine, and when the engine noise is determined as being degraded due to an abnormal combustion, configured to change the target engine noise value to control fuel injection according to the changed target engine noise value.