A method for controlling a cooling system for an internal combustion engine having first and second cooling fans is provided, comprising operating the first cooling fan at a first rotational frequency which is greater than a combustion frequency of the internal combustion engine and operating the second cooling fan at a second rotational frequency which is less than the combustive vibration frequency of the internal combustion engine. Since the rotational frequencies of the first and second cooling fans are different from the combustion frequency of the internal combustion engine, the resonance between the rotational vibration of the cooling fans and the combustive vibration of the internal combustion engine may be prevented. Also, since the rotational frequencies of the first and second cooling fans are different from each other so that the resonance between their rotational vibrations may be prevented.