A control system for a direct alcohol fuel cell, comprising: a fuel tank; a fuel cell stack; a pump feeding the fuel in the fuel tank to the fuel cell stack; a switching mechanism connecting the pump selectively with the fuel and air in the fuel tank; and a control unit switching the switching mechanism to connect the pump with the air when stopping power generation of the fuel cell stack. When the generation of the fuel cell stack is stopped, feeding of the fuel to the fuel cell stack is stopped and the air is supplied to the fuel cell stack thereby pushing out the remaining fuel.