In this paper, newly polyether polyol containing fluorine in the side chain, 6,9-polyoctafluorine hexanoic ether tetradecane glycol (PFEG) was successfully synthesized via cationic ring-opening polymerization method. By means of one-step bulk polymerization method, its mixture with polytetramethylene ether glycol (PTMEG) was used as soft segment to fabricate fluorinated thermoplastic polyurethane (FTPU) elastomers, which were further characterized by SEM, (HNMR)-H-1, FTIR, XRD, contact angle, tensile and thermal stability measurements. Hemocompatibility in vitro was evaluated through protein adsorption and platelet adhesion measurements, while cytocompatibility was assessed by MTT assay and cell adhesion. Results showed that the as-synthesized FTPU elastomers have satisfactory blood compatibility, cytocompatibility, mechanical and thermal stability properties.