Efficient hydrogen flow control is of great importance to ensure the reliable operation of an automotive fuel cell system because it is closely associated with the safety and the economic efficiency. In this study, an effective hydrogen flow control algorithm for hydrogen excess ratio control is addressed by pointing out the recovery speed and overshoot response. Unlike previous studies on the hydrogen management systems of an automotive fuel cell, this study presents an analytic hydrogen tank model which can present the characteristics of the discharge and charge of hydrogen from a type 4 hydrogen tank. To this end, a mode reference adaptive control (MRAC) based on proportional-integral (PI) control is introduced, to ensure robust hydrogen flow during the dynamic operation of fuel cell system. The MRAC was compared with the nominal PI control and PWM control in the hydrogen management system of an automotive fuel cell operating within normal conditions, under steady-state responses and transient. Based on these result, it can further demonstrate that the MRAC algorithm shows better recovery speed and tracking performance than the nominal PI, and PWM control algorithm with respect to the transient behaviors.