In previous study, a new allocation methodology of common cost on multi-product have been suggested. The aim of this study is to suggest the methodology that allocates an environment pollution cost including carbon emission cost to each cost of multi-product. For this study, a supposed multi-energy system composed of twenty kinds of systems was made. The multi-energy system produces eighteen kinds of outputs that are electricity, steam, hot water, chilled water, ice, warm air, and cooling air from seven kinds of energy source that are LNG, coil, geothermal energy, sun heat, hydrogen, bio-mass, and waste. The new methodology was applied to the multi-energy system in order to allocate the environment pollution cost to each production cost, and twenty seven equations were induced. From this result, it is concluded that this methodology can estimate each unit cost and allocate each cost flow in any product of any energy system.