An apparatus and a method of heat exchange of a liquid fuel type fuel cell system. The apparatus includes: an electricity generating unit to generate electricity when a fuel is supplied to an anode and oxidizer is supplied to a cathode; a first flow path unit connected to an outlet of the cathode; a second flow path unit connected to an inlet of the anode; a heat exchanging unit to exchange thermal energy between fluids passing through the first flow path unit and the second flow path unit; a third flow path unit connected to the inlet on an anode and bypassing the heat exchanging unit; and a first valve to control flow ratios of fluids passing through the second flow path unit and the third flow path unit. The method of heat exchange includes: sensing the temperature of the electricity generating unit; and controlling a flow path of the third flow path unit depending on the temperature of the electricity generating unit.