As the efficiency of fuel cell is the ratio of the electrical power output and the fuel input, it can be defined as a function of power density, system pressure, and stoichiometric ratios of hydrogen, and oxygen. Typically the fuel cell efficiency decreases when its power output increases. In order for the fuel cell system to obtain high efficient operation under the same power generation, more cells and other auxiliriaries like a high capacity compressor system and so on are required. In other words, the fuel cell efficiency is closely related to the fuel cell economics. Thus, there should exist a optimun nominal efficiency that results in the cost effective fuel cell system. Using a multi-objective optimization technique, the SQP (sequential quadratic programming) method , the efficiency and the cost of fuel cell system can be optimized under various operating conditions. This paper has already obtained some initial results and will provides a useful suggestion for the design of a cost effiective fuel cell system with a high operation efficiency.