Provided are a method of operating an engine and an apparatus for controlling operation of an engine, which is capable of appropriately controlling the operation of the engine after cutoff of fuel into a cylinder in which heavy knock occurs, without at once stopping the engine upon detection of occurrence of the heavy knock. The method of operating an engine which has a plurality of cylinders, and which is capable of stepwise or continuously correcting a burning state through fuel regulation including cutoff of fuel, upon occurrence of abnormal combustion, executes a stop or an output limit operation of the engine, and is characterized in that a simulated abnormal combustion obtained by calculating an abnormal combustion state of the engine in simulation is beforehand set, and in comparison of a detection signal as to a burning state of a selected cylinder which is sequentially selected among the plurality of cylinders, with the simulated abnormal combustion signal so as to determine occurrence of abnormal combustion in the selected cylinder in order to execute cutoff of fuel into the selected cylinder.