Abstract: In this paper, the hydrophobically-modified copolyester has been synthesized by hydroxy-fluorosilicone polymer (FGX), as the modifier, and dual-hydroxy ester of terephthalic acid oligomer (BHET) via polycondensation. Through the measurement of contact angle, it analyses the relationship between the surface properties of the modified copolymer and the synthesis process route, the viscosity the of modifier and the quantity of modifier. At the same time, Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy and thermal analysis have been used to analysis and discuss the structure of the modified copolyesters. The results of FTIR and 1H-NMR show that the hydrophobically-modified copolyester with chemical bond was formed by FGX and BHET copolymerization, such as by adding 12% of the FGX viscosity 2000CP under low vacuum, the water contact angle of the modified polyester (MPET-12) can be up to 97.2 °,the surface energy of the modified polyester is 23.4mJ/m2, which is close to the FGX’s (20mJ/m2). Due to the small quantities of modifier, the thermal of the hydrophobically-modified copolyester has not changed significantly comparing with Poly(ethylene terephthalate)(PET).