A control system for a variable-cylinder internal combustion engine, which is capable of attaining excellent fuel economy by executing a partial-cylinder operation mode as long as possible, while suppressing vibration and noise during the partial-cylinder operation mode. A control system switches the operation mode of a variable-cylinder internal combustion engine between an all-cylinder operation mode in which all of a plurality of cylinders (#1 to #3, and #4 to #6) are put in operation, and a partial-cylinder operation mode in which some (#1 to #3) of the plurality of cylinders are deactivated. During the partial-cylinder operation mode, the control system 1 calculates a degree-of-continuation parameter SDTQCSNH indicative of a degree of continuation of a state where detected load TQECMDF on the engine is within a predetermined range of load between a first reference value TQCSNH and a second reference value TQCSEH smaller than the first reference value (steps 10 to 13), and determines whether or not the operation mode should be switched to the all-cylinder operation mode, based on the degree-of-continuation parameter SDTQCSNH (step 14).