An apparatus for controlling a temperature of coolant in a water-cooled battery system, includes a heat exchange module including a passage body configured to receive and circulate the coolant from the circulation line, a heat sink disposed outside the passage body, and a thermoelectric element disposed between the heat sink and the passage body; a shaft part separably coupled to the heat exchange module to stack a plurality of heat exchange modules; a frame part separably coupled to the shaft part to close a front surface, a rear surface, an upper surface and a lower surface of the heat exchange module; and a cooling part coupled to one side of the frame part and configured to discharge external air toward the other opened side of the frame part through a gap of the heat sink by at least one cooling fan.