As the world's largest supplier of primary indium, China's indium industrial chain structure and demand change affect global supply. It is necessary to evaluate the security of China's indium industrial chain and determine the reasons that affect security. The past substance flow analysis (SFA) of indium and mineral industrial chain security evaluation has problems such as a lack of timeliness, a single dimension mainly focusing on the upstream, and simple evaluation methods. In this paper, based on the SFA, an integrated evaluation system for the whole life cycle is constructed from 2000 to 2022 according to mineral industrial chain security characteristics. The results show that since introducing liquid crystal in 2003, China's indium industrial chain security level has been low despite a slight increase. Although China has gradually broken through the production technology of high-purity indium and indium tin oxide (ITO) targets, the large consumption and export of refined indium has reduced China's indium metal stock to 2214 t, while the resource reserves advantage is also diminishing. Mass consumption has also led China to import more ores, while China still imports high-end products from other countries with high import source concentrations. The pollutants emitted by the large production and the declining environmental governance level pose a significant environmental threat. Finally, suggestions for strengthening international cooperation, increasing technological research, establishing a reserve system, risk monitoring mechanisms, and strict emission standards can improve China's indium industrial chain security.