Output series interleaved Boost converter (OS-IBC) has become a promising candidate for fuel cell application, due to the features of high voltage gain and low input current ripple. To achieve a satisfactory control performance for the OS-IBC, a robust dual loop control strategy is designed in this paper. The designed controller comprises an inner loop dedicated to inductor current tracking and an outer loop aimed at output voltage regulation, which both based on flatness control. Furthermore, the extended state observers (ESO) are integrated into this control algorithm for online estimating the uncertain input voltage and output current of the equivalent converter. With this ESO, the parasitic circuit parameters are considered into the estimations, and meanwhile the input source voltage sensor and load current sensor can be omitted. The feasibility and robustness of the designed controller have been successfully validated by simulation and experimental results obtained using a 240W prototype converter and a dSPACE control platform.