The polyester containing fluorine in its branch chains was synthesized. First of all, one of the functional groups of 1, 2, 4-phthalic anhydride was capped using 1H, 1H, 2H, 2H-perfluoro-1-decanol, then a part of the pentabutyl diacinate was replaced by terminated 1, 2, 4-phthalic anhydride to obtain fluorinated polyester with neopentyl glycol via copolycondensation reaction. After that, films of the fluorinated polyester were prepared by curing with the crosslinker. The structure, molecular weight and thermal stability of fluorinated polyester were characterized by means of IR, XRD, GPC, TG and DSC. The mechanical properties, surface properties and surface element content of fluorinated polyester films were assessed by using universal testing machine, contact angle tester and X-ray electron spectroscopy. The results show that with the increase of the functional groups, the molecular mass of fluorinated polyester increased compared with the non-fluorinated polyester, while the thermal stability of fluorinated polyester increased firstly and then decreased; The maximum initial decomposition temperature is as high as 299.41℃;The glass transition temperature was gradually increased from 6.24℃ to 46.65℃; the elongation at break of fluorinated polyester film decreased while the tensile strength increased gradually, and the maximum tensile strength reached 19.97 MPa. The fluorinated groups migrated from the main body to the surface of the fluorinated polyester film. Furthermore, the water contact angles and the oil contact angles of films increased with the increase of fluorinated groups while the films gained hydrophobicity.