A cooling system for vehicles and a control method thereof improves indoor heating performance and fuel efficiency by controlling a flow rate of a coolant passing through a heater core together with an EGR cooler. A coolant having an increased temperature is first supplied to the heater core side through a flow stagnancy control to rapidly increase the temperature of the coolant flowing in the heater core, thereby improving heating performance. A warm-up feature is improved through an exhaust heatrecovery function by a heat exchange between the exhaust gas and the coolant in the EGR cooler, thereby improving efficiency of fuel.