In this paper, an innovative robust dual loop control strategy for the non-ideal Boost converter subject to load resistance disturbances and input voltage variation is successfully developed and implemented. By converting the power losses of non-ideal Boost converter into serial and parallel resistance, the equivalent circuit and its mathematical model are established. Then, for the outer voltage loop, a flatness based control incorporated with a parameters estimation technique used to estimate the unknown input voltage and output current is designed to assure tight reference voltage tracking under the extern disturbances. Meanwhile, a rigorous stability proof based on the Routh-Hurwitz criteria is given. Moreover, for the inner current loop, a simple PI controller is employed to achieving the reference current tracking. Finally, the validity and robustness of the proposed control scheme and parameters estimation accuracy are verified through numerical simulation.