Abstract: As an important resource for the development of modern industry, rare earth elements are widely used in nuclear technology, batteries, permanent magnet, electronic products, catalysis, and superconducting technology, and they have been mined at a considerable large scale. China’s rare earth resources are abundant, and their reserves account for approximately 36.7% of the world’s total reserves. Over the recent years, global rare earth resources are generally faced with over-exploitation, low utilization rates, and serious environmental pollution problems. Therefore, there is an urgent need for the development of recovery systems that are inexpensive and cause less pollution. Rare earth elements can be widely involved in the metabolism of compounds in various micro-organisms and may have mining capabilities. The use of microbial technology to mine and recover rare earth resources has provided a novel green and efficient method for the utilization of rare earth resources, and research in related fields has continued intensify. This paper primarily introduced the important role and utilization status of rare earth resources, summarized the distribution and characteristics of rare earth minerals in China, and identified the problems associated with rare earth mining and the advantages of microbial mining. Furthermore, it reviewed the development process of rare earth mining using micro-organisms, summarized its research progress, and introduced the research mechanism of microbial mining, primarily including related research on the mechanism of microbial leaching, adsorption and accumulation of rare earth elements, separation methods, species distribution, and mechanism action of rare earth ore mining microorganisms. Considering minerals of the Bayan Obo deposit in China and the Mount Weld deposit in Australia as examples, the extraction of rare earth elements from ore by microbes selected from the surrounding environment has been explained. Moreover, the recovery of rare earth elements in low-grade ore and waste by micro-organisms has been briefly described. Based on the current status of microbial mining of rare earth ore, future challenges and prospects of microbial utilization of rare earth elements have been proposed.