In China, coal fly ash (CFA) is the third-largest industrial waste and causes significant economic and environmental problems. Based on the technology of extracting alumina co-generated with calcium silicate and calcium silicon slag cement clinker, a multi-resource utilization of high-alumina coal fly ash system (MUCFA) is developed and thought to be a promising approach to utilize CFA. As a solid waste utilization system, the environmental effects of MUCFA, particularly heavy metal pollution, will significantly affect its promotion and development. Therefore, an integrated substance flow analysis (SFA) model is proposed to investigate the heavy metal flows and associated environmental effects of MUCFA. With the combination of sampling test and SFA, migration paths of heavy metals are figured out. The results of value flow analysis and environmental impact assessment depict an outline of MUCFA and indicate that CFA accounts for 24 % of the environmental impact and is not the major source of environmental impact. Chromium (Cr) and lead (Pb) exhibit similar migration paths but differ in the distribution rate of the processes. 57 % of the total Cr and 53 % of the total Pb are migrated into calcium silicon slag, while 24 % of Cr and 33 % of Pb are found in flue gas. In order to eliminate the potential environmental problems, some retrofits are implemented to optimize the heavy metal migration pathway. Moreover, several suggestions on making standards and regulations for waste utilization are provided to both government and companies for the development of MUCFA.