Fuel cells with zero-emission and high-efficiency have been the most promising new alternative energy resource for electric vehicles and distributed generation applications. However, due to the lower and unregulated output voltage of fuel cell and the strict requirement for the input current ripple, an output series interleaved Boost converter (OS-IBC) with high voltage gain and low input current ripple is utilized as an interface between fuel cell and high voltage DC bus. Furthermore, in order to deal with the intrinsic nonlinearity and non-minimum phase phenomenon of OS-IBC, while achieving a desired dynamic performance, a dual loop control including an inner current loop using nonlinear super-twisting control and an outer voltage loop with nonlinear flatness-based control is proposed and designed in detail in this paper. Meanwhile, the stability of the current loop and the voltage loop are proved based on Lyapunov stability theory and Routh-Hurwitz criteria, respectively. Finally, the simulation results obtained by using Matlab/Simulink allow validating the effectiveness and the robustness of the proposed control strategy.