In the present paper the structure of a single inductor double output converter (SIDO) has been studied. One of the major challenge, to design a controller in SIDO Converters, is removing the cross-regulation among the outputs. On the other hand, the multi-stages operation of SIDO converters cause, to achieve the model which predicts their all behaviors, be more difficult than typical converters. In this paper a SIDO Boost/Boost converter is modeled by a systematic signal flow graph (SFG) modelling. Based on obtained model a multivariable control scheme has been proposed to reduce the cross regulation of the output. Finally Simulation results are included to show the validity of the obtained model and the designed Controller.