Rare earth elements (REEs) are essential elements in many technology industries. The commonly used ammonium salt method has caused a bad impact on environment. Bioleaching is widely recognized as a low energy, relatively simple and environmentally friendly method. The purpose of this work is to extract REEs from ion-adsorption type rare earth ore by using three different bioleaching methods (one-step, two-step, and spent medium method, respectively) and the strain used was Aspergillus niger strain. Major organic acids produced during microbial growth were detected and the REEs leaching efficiency of three methods was compared. In addition, the interaction between the strain and their metabolites and rare earth ore was investigated by FT-IR, XRD, SEM-EDS, and TEM-EDS during the leaching process. In the end, it was found that the spent medium method had the best leaching effect, and various characterization methods showed that the three bioleaching methods had obvious changes before and after leaching, among which the spent medium method had the most significant effect. Additionally, through the analysis, it can be concluded that the complexation and acidolysis may occur in the bioleaching process.