The evolution of energy system occupies an important position in economic development and quality of life. Influenced by the energy endowment in China, developing the coal-based clean energy industry has been regarded as a guaranteed path to realizing the clean and efficient use of coal resources. However, an evaluation paradigm could systematically assess the health impacts of airborne pollution in this industry is still lack, which is our concern. Combining with life cycle analysis, probabilistic risk models, and health impacts models, this study proposes a series of models which are consistent enough to unite pollutant concentration, health risk, and health impact, and equip assessment results with more intuitive significance using life and economic loss. Further, case studies for three typical coal-based clean energy processing, namely, coal mining, coal-fired power generation, and coal liquefaction are presented to verify the reliability of these models. It is proved that this evaluation paradigm can help to find out the worksite, substage, and airborne pollutant with the most severe impact, and more importantly, the application of evaluation indicators with life and economic meaning is more profitable to provide references for minimizing or eliminating the health impacts, moreover, explicit the developing directions of the national energy industry.