The poly(aryl ether ketone) containing trifluoromethyl in the main chain (m-F-PAEK) and side chain (s-F-PAEK) were respectively synthesized through nucleophilic polycondensation. The structures of the two poly(aryl ether ketone)s were determined by 1H-NMR. DSC studies showed that Tg of the m-F-PAEK was 166oC, and that of the s-F-PAEK was 139oC. The higher Tg of m-F-PAEK was due to the trifluoromethyl in the main chain which had increased the rigidity. Moreover, the 5% thermal weightless temperature of the two polymers was above 490oC, indicating their good thermal stability. Water contact angle results showed that the water contact angle of the m-F-PAEK and the s-F-PAEK was 91o and 113o, respectively. The result demonstrated that s-F-PAEK had better hydrophobic performance than m-F-PAEK. This was because that the fluorine atoms of the s-F-PAEK more likely to migrate to the surface of the film after high temperature treatment, which decreased the surface energy further.