In this study, a novel approach for dynamic modeling and closed-loop control of hybrid grid-connected renewable energy system with multi-input multi-output (MIMO) controller is proposed. The studied converter includes two parallel DC-DC boost converters, which are connected into the power grid through a single-phase H-bridge inverter. The proposed MIMO controller is developed for maximum power point tracking of photovoltaic (PV)/fuel-cell (FC) input power sources and output power control of the grid-connected DC-AC inverter. Considering circuit topology of the system, a unique MIMO model is proposed for the analysis of the entire system. A unique model of the system includes all of the circuit state variables in DC-DC and DC-AC converters. In fact, from the viewpoint of closed-loop controller design, the hybrid grid-connected energy system is an MIMO system. The control inputs of the system are duty cycles of the DC-DC boost converters and the amplitude modulation index of DC-AC inverters. Furthermore, the control outputs are the output power of the PV/FC input power sources as well as AC power injected into the power grid. After the development of the unique model for the entire system, a decoupling network is introduced for system input-output linearization due to inherent connection of the control outputs with all of the system inputs. Considering the decoupled model and small signal linearization, the required linear controllers are designed to adjust the outputs. Finally, to evaluate the accuracy and effectiveness of the designed controllers, the PV/FC based grid-connected system is simulated using the MATLAB/Simulink toolbox.