Disclosed herein is a direct methanol fuel cell system. More particularly, the present invention provides a water controller system constructed such that water generated from a cathode of the direct methanol fuel cell system and carbon dioxide and an unreacted methanol solution generated from an anode of the direct methanol fuel cell system are introduced into the water controller system, the carbon dioxide is discharged out of the water controller system, and the methanol solution is circulated to the corresponding electrode so as to reuse the methanol solution, and a fuel cell system including the water controller system. The water controller system for fuel cells according to the present invention has the effects of reusing water and an unreacted methanol solution discharged from the fuel cell, minimizing the amount of methanol evaporated and discharged, and accurately controlling the water level of the water controller.