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Rare earths are a kind of mineral resource with important strategic value, playing an irreplaceable key role in modern high-tech development and other fields. However, how to realize the efficient and green mining of rare earth resources has been a key issue that the rare earth industry has been trying to break through, because the rare earth mining process is prone to pollute ecological environments such as soil and water. Ion adsorption rare earth ore, mainly distributed in the south of China, is one of the rare earths, for which rare earth researchers have developed a new process leaching system with magnesium salt. In this study, the soil environmental problems as well as the microbial community structure underneath this new process heap-leaching demonstration site are evaluated. The results of the study showed that under the new process, there was a significant accumulation of sulfate content in the soil of the heap-leaching site and an imbalance in the soil calcium-magnesium ratio, which may disrupt the soil structure and reduce soil fertility. Meanwhile, the microbial community structure before and after the leaching site showed large differences at different points and depths, but didn't cause ecological risks. This study helps us to understand the environmental problems and impacts that may be caused by the new process of magnesium salt, and also helps to promote the application of the new process of magnesium salt leaching of ion adsorption rare earth ore, which lays the foundation for the exploitation of rare earth resources.