Ion adsorption rare earth ore nearly satisfy global market demand for heavy rare earth elements (HREEs). Bio-leaching has important potential for the clean and efficient extraction of ion-adsorption rare earth ore. However, the complexities of in-situ mining restrict the use of contact/direct bio-leaching, and non-contact/indirect bio-leaching would be the best choice. This study explore the potential of fermentation broths prepared by Yarrowia lipolytica (ATCC 30162) for the bio-leaching of ion-adsorption rare earth ore, and three typical metabolites (potassium citrate (K3Cit), sodium citrate (Na3Cit) and ammonium citrate ((NH4)3Cit) of Yarrowia lipolytica were further evaluated in simulated bioleaching (non-contact bioleaching) of ion-adsorption rare earth ore, including leaching behavior, seepage rule and rare earth elements (REEs) morphological transformation. The column leaching experiments shown that direct leaching of REEs using fermentation broths results in incomplete leaching of REEs due to the influence of impurities. Using the purified and prepared metabolites as lixiviant, REEs can be effectively extracted (leaching efficiency >90%) at cation concentration was only 10 % of the commonly used ammonium sulfate concentration (45 mM). Cation type had less effect on leaching efficiency. During the ion-adsorption rare earth ore leaching process, rare earth ions form a variety of complex chelates with citrate, thus transferring rare earth elements from the mineral surface to the leachate. Experimental results showed that pH and concentration together determined the type and form of rare earth chelates, which in turn affect the leaching behavior of REEs and solution seepage rule. This study helps to provide a theoretical basis for the regulation and enhancement of ion-adsorption rare earth ore non-contact bioleaching process.