A fuel cell system enabling waste heat recovery includes an air supply unit and a fuel supply unit for supplying required air and methanol/water mixture, respectively, to the fuel cell stack for reaction. The methanol/water mixture is then expelled from the fuel cell stack after having been used in the reaction in the fuel cell stack. The methanol/water mixture is supplied to the fuel supply unit from a mixing tank, into which pure methanol and water are separately supplied and then mixed. Waste gas produced in the reaction in the fuel cell stack is expelled from the fuel cell stack and led into the mixing tank to evenly mix with the methanol/water mixture. Reaction heat produced in the reaction in the fuel cell stack may be recovered to heat the air supplied to the fuel cell stack to thereby upgrade the performance of the fuel cell stack.