A series of fluorinated waterborne polyurethane (FWPU) with various lengths of fluorinated side chains were synthesized by using different fluoro alcohol-terminated isocyanate trimer (F-HDIT) which prepared from hexafluoroisopropanol (HFIP), 2,2,3,3,4,4,5,5-octafluoropentanol (OFP), 3,3,4,4,5,5,6,6,7,7,8,8,8-tridecafluoro-1-octanol (TFO) and hexamethylene diisocyanate trimer (HDIT). The influences of fluorocarbon chains' length and fluorine content on the properties of FWPU, involving contact angle, surface energy of film and critical surface tension of emulsion were well-investigated in detail. The XPS result showed that the surface atom percentage of fluorine element of film increased from 0.58 for 6FWPU-5 to 28.19 for 13FWPU-20 with the escalation of F-HDIT content and the length of fluorocarbon lateral chain, which results in the water contact angle increment and surface energy reduction of FWPU films. Similarly, along with the increase of F-HDIT content and fluorocarbon side chains' length, the surface tension of FWPU emulsion exhibited a downtrend with the order of 13FWPU-20 (33.4 mNm(-1)) < 8FWPU-20 (36.5 mN.m(-1)) < 6FWPU-20 (36.9 mN.m(-1)) < FWPU-0 (40.0 mN.m(-1)). Besides, the enrichment of fluorocarbon chains can be deduced from AFM 3D morphology. The control sample FWPU-0 showed a relatively smooth surface while FWPU samples exhibited spike-like surface, indicating that the migration of fluorine side chains might increase the surface roughness of FWPU films.