In this paper, a disturbance observer (DOB) algorithm is proposed to solve the output voltage regulation of an Interleaved Boost Converter (IBC) in presence of unknown disturbance and parameter uncertainty. IBCs are improved model of boost converters which provide better operation than conventional converters. Also, these converters are rather complicated, therefore, the modeling of them are more cumbersome. To solve this problem, the Signal Flow Graph (SFG) method is implemented for a 2-cells IBC. The main advantage of SFG is obtaining unified dynamic mode of converter. Beside the modeling problem, unknown disturbances such as the input voltage ripple, mismatching of duty cycles and load variations are inevitable in real circuit and degrade the system performance. To obtain a high performance regulation in presence of disturbances, a DOB is integrated with an optimal controller. According to our models, the duty cycle variation is limited so an optimal control technique is implemented to achieve a good tracking. Furthermore, the DOB can be estimate and compensate the unknown disturbances. Simulation results for a real model of a 2-cells IBC indicates that application of DOB and SFG modeling is quite effective in correct performance of IBC in presence of unknown disturbances.