With the development of the steel industry, China’s demand for niobium is increasing. However, domestic niobium resources are not yet stably supplied and are heavily dependent on imports from abroad (nearly 100%). It is urgent to develop domestic niobium resources. The Bayan Obo deposit is the largest rare earth element deposit in the world and contains a huge amount of niobium resources. However, the niobium resource has not been exploited due to the fine-grained size and heterogeneous and scattered occurrences of Nb minerals. To promote the utilization of niobium resources in the Bayan Obo deposit, we focused on the mineralogical and geochemical characterization of six types of ores and mineral processing samples from the Bayan Obo deposit, using optical microscopes, EPMA, TIMA, and LA–ICP–MS. Our results show that: (1) the niobium mineral compositions are complex, with the main Nb minerals including aeschynite group minerals, columbite–(Fe), fluorcalciopyrochlore, Nb–bearing rutile, baotite, fergusonite–(Y), fersmite, and a small amount of samarskite–(Y). Aeschynite group minerals, columbite–(Fe), and fluorcalciopyrochlore are the main niobium-carrying minerals and should be the primary focus of industrial recycling and utilization. Based on mineralogical and geochemical investigation, the size of the aeschynite group minerals is large enough for mineral processing. Aeschynite group minerals are thus a significant potential recovery target for niobium, as well as for medium–heavy REE resources. The Nb–rich aegirine-type ores with aeschynite group mineral megacrysts are suggested to be the most significant niobium resource for mineral processing and prospecting. Combined with geological features, mining, and mineral processing, niobium beneficiation efforts of aeschynite group minerals are crucial for making breakthroughs in the utilization of niobium resources at the Bayan Obo.