A method for controlling a cooling system in a vehicle, may include an Exhaust Gas Recirculation (EGR) use determination step of determining whether to use EGR, a first coolant temperature management step of controlling a coolant temperature using a first coolant temperature map based on an output value reflecting engine operating conditions when driving the vehicle using the EGR, and a second coolant temperature management step of controlling the coolant temperature using a second coolant temperature map in which a coolant temperature of the second coolant temperature map may be set to be higher than a coolant temperature of the first coolant temperature map in a same engine operation region when driving the vehicle not using the EGR.