The present disclosure provides a method and system, for controlling a coolant circulating in an engine, including: selecting a reference inlet temperature for a coolant flowing through a coolant inlet of an engine; controlling an open rate of the coolant control valve unit based on the reference inlet temperature; sensing an actual inlet temperature of the coolant flowing through the coolant inlet of the engine; sensing an actual outlet temperature of a coolant flowing through a coolant outlet of the engine; calculating a difference value between the actual inlet temperature and the actual outlet temperature; and varying the reference inlet temperature according to the difference value.