A control method of a magnet type fan clutch is provided to improve engine performance, fuel economy, engine life, and vehicle acceleration and to reduce fan noise, and optimize fan horsepower. The magnet type fan clutch has a magnet coupling combined with an electromagnetic clutch. The method includes turning the electromagnetic clutch ON and OFF on the basis of cooling fluid temperature, engine oil temperature, transmission oil temperature, vehicle speed, engine rotation rate, accelerator opening, compressor pressure of an air conditioner, an On or Off signal of the air condition, a fuel injection indication amount, a clutch activation lower limit temperature and its lower temperature, and an engine rotation rate set value to control the fan rotation.