The integrated system of a solid oxide fuel cell and molten carbonate fuel cell theoretically has very good potential for power generation with carbon dioxide utilization. However, the control strategy of such a system needs to be considered for efficient operation. In this paper, a control structure design for an integrated fuel cell system is performed based on economic optimization to select manipulated variables, controlled variables and control configurations. The objective (cost) function includes a carbon tax to get an optimal trade-off between power generation and carbon dioxide emission, and constraints include safe operation. This study focuses on the top-down economic analysis which is the first part of the design procedure. Three actively constrained regions as a function of the main disturbances, namely, the fuel and steam feed rates, are identified; each region represents different sets of active constraints. Under nominal operating conditions, the system operates in region I. However, operating the fuel cell system in region I and II can use the same structure, but in region III, a different control structure is required.