A preparation method of an ionic rare earth leaching agent includes the following steps: (1) domestication microorganisms with rare earth activated mineral powder culture medium to obtain a microbial suspension; (2) amplifying and culturing the microbial suspension and additives to obtain the amplified culture medium; and (3) mixing the modified sesbania gum with the amplified culture medium to obtain the ionic rare earth leaching agent. The activated mineral powder is the active metal-containing mineral powder in nature, which has excellent cation exchange function after activation, and the activated mineral powder and ionic rare earth mineral powder are used as the medium components to domesticate microorganisms, so that microorganisms can survive in the above-mentioned ionic solution and improve the leaching rate of synergistic leaching ionic rare earth.