The electric vehicle technology has been adopting PEM fuel cells for hybrid applications over the past decades. Fuel cell systems are often low voltage systems. The key requirements of a boost converter for such application are need of high-voltage. The second-order low-pass filter is often used to filter the high frequency current ripple. It is known that the interaction between the poorly damped filter with the converter leads to degradation of dynamic performance and instability of the system. This paper addresses a novel wide stability control strategy to solve this problem without increasing the weight and size. In this paper, the mathematical model of the system is built. The dynamic stability of the system is investigated based on root locus and Lyapunov first method. The simulation results are reported to verify the effectiveness of the proposed method.