For the development of sustainable and efficient separation technology for rare earth elements (REEs), the ionic liquid-type saponification strategy is first put forward in this paper. The extraction mechanism of [trihexyl(tetradecyl)phosphonium][sec-octylphenoxy acetate] ( [P 6,6,6,14 ][SOPAA]) prepared by ionic liquid-type saponification for Y(III) was indicated to be ion association. The mechanism contributes to avoiding the numerous saponification procedures and resulting saponification wastewater in the REE separation industry. Load capacity and stripping properties of [P 6,6,6,14 ][SOPAA] reveal advantages over its precursory sec-octylphenoxy acetic acid (HSOPAA). Extractability and selectivity of [P 6,6,6,14 ][SOPAA] for Y(III) are pronouncedly better than those of HSOPAA. Multistage extraction using functional ionic liquid as extractant for different REE separations is developed. After five stages of extraction sections and four stages of scrubbing sections, Lu(III) was successfully separated from Y(III) using the fractional extraction process. Moreover, stripping by distilled water was achieved in ionic liquid-based extraction for REE, which contributes to decrease the consumption of acid to a considerable extent.