The invention provides a fuel supply control system for fuel cells, controlling fuel concentration in a fuel unit. The fuel supply control system comprises a first thermal meter detecting a system temperature of the fuel cell, a fuel supply device comprising a fuel tank storing highly concentrated fuel and a fuel deliver device delivering fuel from the fuel tank to the reaction unit to adjust fuel concentration thereof, and a controller calculating a difference between a predetermined and an environmental temperature, generating a first velocity by adjusting the predetermined fuel supply velocity according to the temperature difference, and setting the delivery velocity of the fuel delivering device according to the first velocity.