Eight functionalized ionic liquids (ILs) prepared by trihexyl(tetradecyl)phosphonium chloride ([P-6,P-6,P-6,P-14]Cl) and phenoxy dicarboxylic acids were studied for valuable metal recovery in this paper. The effects of alkyl chain length and its structural isomerism on the physicochemical properties of the ILs were determined. It was found that the ILs had higher extractabilities to RE[La(III), Nd(III), Eu(III), Lu(III), Y(III)], Cu(II), and Zn(II) than some other metal ions [Mg(II), Ca(II), Sr(II), Mn(II), Co(II), and Ni(II)]. Moreover, Cu(II) and Zn(II) could be easily stripped from the RE(III)-loaded ILs using ammonium hydroxide solution. Further experiments showed that the weakly extracted metal ions could be effectively scrubbed and stripped with NaCl solution, thereby preferentially extracting metals with high purities. The applications of the proposed recovery systems were effectively demonstrated by the fact that 100 wt % Cu(II) and 99.9 wt % La(III) could be obtained in the separation process of Cu(II)/Co(II) and La(III)/Ni(II), respectively.