An engine control system of a multiple cylinder engine shifts operation between operation with all the cylinders operated and operation with a portion of the cylinders rested under a predetermined condition. When the operation with all the cylinders operated is shifted to operation with the number of the operating cylinders reduced, a control value for controlling the cylinder, such as an amount of fuel to be supplied or an ignition timing, is corrected in a direction of increasing output of the engine, the cylinder being in process of combustion immediately prior to a shift from the operation with all the cylinders operated to the operation with the number of the operating cylinders being reduced.