A ventilation system and a controlling method of such a ventilation system are provided. The ventilation system may exhaust internal air from and draw fresh external air into a designated space. When an outdoor temperature is below a freezing point, some of the internal components of the ventilation system may be damaged due to the low external air temperature. This ventilation system controls operation of a supply fan and/or an exhaust fan based on the temperature of supplied and/or exhausted air to prevent such damage.