As greenhouse gas (GHG) reductions have become a major global issue in energy industry, interest in GHG emission trading schemes (ETSs) has increased. In this study, an ETS for cogeneration businesses in the industrial complex of South Korea is discussed. In the cogeneration businesses, power generation is related to the quality of supplied heat which is determined by the industrial heat demand and should be different levels of heat required to the demand side. However, Alternative Generation Method (AGM) or Power Bonus Method (PBM), the popular enthalpy-based methods, cannot reflect the quality of heat properly since it deems the weight for the amount heat highly, little consideration for quality. To reflect the quality of heat, we compared the following three exergy-based calculation methods; Carnot method, Exergy Efficiency Method (EEM), and Exergy-based Power Bonus Method (EPBM). An ideal case was used to evaluate the variation in allowances produced by the allocation methods for different supply temperatures of a combined heat and power (CHP) plant. Then, a case using real data from cogeneration businesses in the industrial complex of South Korea was analyzed. According to the evaluation, EEM was found to be the most appropriate method for managing the cogeneration businesses.