The present study proposes a new method for real time estimating the methanol concentration of a direct methanol fuel cell stack. Using the relations of the methanol crossover quantity with the methanol concentration of the input fuel and with the activation parameters of a fuel cell stack when operating in an interrupt mode, we establish the relationship of the fuel methanol concentration with the interrupt mode activation parameters of a fuel cell stack. With these relationships, we can real-time estimate the fuel methanol concentration and thus control the input fuel methanol concentration. By using this sensor-less methanol fuel control system, we are thus able to reduce the system volume, fuel consumption, and design cost of a micro-fuel cell system. We also expect that the simple and precise methanol feeding control system could allow us to have stable parameters for the thermal and water managements.