The invention discloses a system and a method of cooling an engine of a vehicle. The method of cooling the engine of the vehicle includes measuring a temperature of a cylinder head of the engine, determining whether the measured temperature of the cylinder head may be equal to or lower than a predetermined temperature, when the temperature of the cylinder head may be equal to or lower than the predetermined temperature, moving coolant of the cylinder head and a cylinder block to a separate coolant tank, determining whether the measured temperature of the cylinder head may be equal to or higher than a specific temperature, and when the measured temperature of the cylinder head may be equal to or higher than the specific temperature, supplying coolant stored in the coolant tank to the cylinder head or the cylinder block.