Perfluoropolyether (PFPE) polymers potentially improve the thermodynamic stability, compatibility, and ionic conductivity of sulfide-based solid-state electrolyte (SSE)/Li-metal interfaces. However, ion-transport kinetics of PFPE polymers remain inadequately understood. Using molecular dynamics, we characterized the coordination structures and diffusion in PFPEs terminated with hydroxyl or carboxyl moieties and poly(ethylene oxide) (PEO) embedded with lithium and bis(trifluoromethylsulfonyl)imide ions. The mechanism underlying Li+ diffusion in the PFPE polymers was found to differ from that in PEO, and their respective ion–polymer contact strengths and durations were analyzed. Furthermore, the terminal structure of PFPE polymers was shown to significantly alter the cation–polymer and anion–polymer coordination structures, which in turn accounts for the different extents of the Li+ coordination strength in PFPE-diol and PFPE-dimethylcarbonate (DMC). Finally, PFPE-DMC favors longer durations of contact with cations and shorter ones with anions, whereas this relationship is reversed in PFPE-diol. Thus, we provide a novel way to explain experimentally the observed differences in their ionic conductivities, and we illustrate a general principle for increasing Li+ diffusivity in PFPE polymers, providing an avenue for understanding ionic migration in PFPE–SSE composite electrolytes.