Coal-fired power generation is the main source of waste dust and acid gas emissions. As a case of a certain 2×600MW supercritical power generation units, according to traditional emergy indices system, simply power generation system, power generation system with dedusting system and power generation system with dedusting and desulfurization system were analyzed. The results have showed that although waste recycling systems were installed in coal-fired power generation system, Emergy Sustainability Index(ESI) decreased. Therefore,traditional emergy indices system has not been suitable for sustainable evaluation of the coal-fired electrical power generation system,which produces so much waste. On the basis of this character, the corresponding indices were put forward for reflecting coal-fired electrical power generation system, including Effective Emergy Yield Ratio(EEYR), Emergy Environment Influencing Ratio(EEIR) and Effective Emergy Sustainability Index(EESI). The EEIR of the three power generation system were 2.249、2.628、2.642, respectively. With the increase of waste treatment level, the sustainability of system was better that showed the positive significance of the investment in environmental protection systems.