Recently, due to the use of fossil fuels for electric power production, carbon emissions increased excessively. Thereby, in order to replace fossil fuels, many studies about fossil fuels such as solar and fuel cell energy source are progressing. Fuel cell system has high energy conversion efficiency. Also, fuel cell system is environmentally friendly system because the carbon emission is almost not occur. Therefore, the fuel cell system is considered as the core technology of in the fields of the future energy and environmental. Fuel cell system has an effect on distribution power system because another power source of other than large power plants. So, fuel cell system can be degradation reason of power quality in the power system. In this paper, we constructed the system for an assessment on harmonics effect. The system is composed with power source, harmonics generation and linear load, fuel cell system. we also performed assessment on harmonics effect in customer and the distributed power system during grid connection of residential fuel cell system. An assessment cases are divided into three. A Case 1 is state that residential load and fuel system are connected to grid, Case 2 is state that residential load and harmonics load are connected to grid, and Case 3 is state that all loads are connected to grid. As a output of fuel cell system is increase, analysis results based on assessment system showed that power quality became more aggravation as effect of harmonics.