Conventional polymer inclusion membranes (PIMs) exhibit suboptimal mechanical properties. Consequently, new composite PIMs were prepared by a modified solvent evaporation method using a PTFE base membrane, a PVC polymer, and an organic phosphonate extractant. Their chemical compositions and microstructures were analyzed by ATR-FTIR and FESEM. The mechanical and mass transfer properties of the composite PIMs were systematically investigated. The composite PIMs exhibited significantly higher tensile strength (36.86 MPa to 52.77 MPa), reduced tensile strain (76.49 % to 118.49 %), and enhanced bursting strength exceeding 0.2 MPa, compared to conventional PIMs. The Zn2+/Cu2+ were separated with a high separation coefficient of 2003.19 by a retardant-enhanced composite PIM system. A new mass transfer model was developed by analyzing the multilayered structure of composite PIMs in depth. The apparent diffusion coefficient of Zn2+ within PTFE-PVC composite layer (7.76 × 10−14 m2/s) was found to be lower than that within polymer inclusion layer (3.18 × 10−13 m2/s). The optimal regions of polymer inclusion layer thickness, contact area, and time were selected by model calculation for a certain separation task (e.g., purity ≥ 0.97 and yield ≥0.80 for Zn2+ or Cu2+). Finally, the retardant-enhanced composite PIMs were successfully used for selective separation of several other transition metal ions.