Substance flow analysis (SFA) can quantify relationships between the economy and the environment of a geographically demarcated system. It characterizes the pathways of a substance or group of substances in, out and through that system, which makes it an effective tool to support the resource and environmental management. The study defines SFA and then introduces its evolution process. After that, the paper explains the methodology in detail; followed by discussing its application. The results show that SFA is an important tool for industrial ecology paradigm. It can be applied to 1) trace the pathway of contaminants and analyze their effect on the environment, 2) evaluate the utilization of strategic resources in anthroposphere and 3) estimate in-use stocks of critical substances. In the end, the research examines the perspectives on the research and application of SFA in future.