The necessity of the low carbon society has been more significant since Toya Lake summit was held in Hokkaido, Japan. Under the circumstances, the biomass energy system and/or fuel cell system are promising systems for CO2 emission mitigation. In order to promote PEFC-CGS (Polymer Electrolyte Fuel Cell Co-generation), on the promotion of PEFC-CGS, we have to solve the discrepancy between the supply and the demand. In this paper, the operating cost, the equivalent CO2 emissions including N2O emissions and CO2 abatement cost for the greenhouse facility of strawberries in which PEFC-CGS was installed were analyzed. Through the Blue Tower process, which is one of gasification processes, the high concentration hydrogen gas (Bio-H2) is synthesized. The PEFC-CGS operation using Bio-H2 fuel, that is, the PEFC-CGS combined with BT gasifier would be extremely significant for the realization of low carbon emission society. In our analyses, the green house scale was assumed to be 1 to 5 ha. As a result, the power efficiency and the heat recovery efficiency were 24.0 LHV-% and 22.1 LHV-%, respectively. Also, the annual CO2 emissions in the case of 1ha green house were 2,350t-CO2/yr, and the abatement cost range was between 7,675 and 33,393 JPY/t-CO2.