The control system of molten carbonate fuel cell (MCFC) coupled with a gas turbine (GT) should be based on the multilayer structure (two- or three-layers), wherein the third layer is connected with the power output from the system and can be considered separately. Simulation model of the MCFC–GT hybrid system (HS) was built. The simulator is based on a zero-dimensional modeling of the individual elements of the system. The simulator was used for mapping the main components behavior (MCFC and GT separately). On the basis of the obtained maps of the performances and adopted restrictions on technical–operational nature, the operation line for the first line of the control strategy was obtained. The control system which realizes the obtained control strategy was built in reality. Then, the hardware-based models of the main elements were created based on the electric equipment. The hardware–software model was connected to the control system and adequate simulations were performed. The presented results indicate that the analyzed MCFC–GT HS possesses a high operation and control flexibility while at the same time maintaining stable thermal efficiency. Operation of the system is possible over a wide range of parameter changes.