Fluorinated aliphatic polyurethanes based on hexamethylene diisocyanate (HDI) and polytetramethyl oxide (PTMO) were synthesized by using 2,2,3,3,4,4,5,5‐octafluoro‐1,6‐hexanediol (OF) or 2,2,3,3‐tetrafluoro‐1,4‐ butanediol (TF) as a chain extender. The polyurethanes chainextended with 1,4‐butanediol (BD) were also prepared for comparison. The effects of the kind of chain extender and the average length of hard segments on the microstructure, thermal transition property, surface property and blood compatibility of the polyurethanes are discussed. The fluorinated polyurethanes exhibit weaker hydrogen bonding, a smaller fraction of hydrogen‐bonded carbonyls, less phase separated soft segment domains, a lower melting temperature and less heat of fusion of crystalline hard segment domains than the polyurethanes chain extended with BD. The polyurethanes extended with OF show the above mentioned effects more obviously than those with TF. The increase of the average length of hard segments also affects the properties, especially as the average length of hard segments increases from 1 to 2. The polyurethanes chain extended with OF posses more fluorocarbon chains at the surface than those chain extended with TF. The hard segment content of the surface and the fluorine/carbon atomic ratio increases as the bulk average length of hard segments increases. In vitro platelet adhesion studies indicated that the addition of fluorocarbon chains into aliphatic polyurethanes leads to a reduction in platelet adhesion and activation.