Industrial flue gas systems include fine soot and high-temperature vapor. The continuous emission of the flue gas not only causes fine particulate pollution but also wastes considerable heat energy. Separating soot and purifying flue gas are of great significance for industrial conditions and environmental protection. In this paper, the process of cyclone soot elimination and waste heat recovery by heterogeneous condensation were coupled for the first time. The effects of the flue gas material system and separation operation parameters on the cyclone soot elimination efficiency and heat transfer efficiency were systematically investigated through unit experiments and industrial side-lines. Additionally, the mechanism of enhanced cyclone soot elimination by heterogeneous condensation was also theoretically explored. The experimental results show that the corresponding maximum cyclone heat transfer efficiency and soot elimination efficiency of the Ф40 mm cyclone separator are 42.1% and 89.2%, respectively, while the Ф80 mm cyclone separator can attain an elimination efficiency of 91% and a maximum increase of 67.3% for the heat transfer efficiency, as indicated by the industrial side-line. During the process of cyclone soot elimination and heat recovery by heterogeneous condensation, the heterogeneous condensation caused by heat transfer increases the quality difference between the flue gas molecules and soot droplets, thus improving the cyclone separation efficiency of soot.