Sulfonated poly(ethylene glycol) (PEG-$SO_{3}$) grafted polyrotaxanes (PRx-PEG-$SO_{3}$) were prepared in order to utilize the unique properties of PEG-$SO_{3}$ and the supramolecular structure of PRx, in which PEG-$SO_{3}$ grafted $alpha$-cyclodextrins ($alpha$-CDs) were threaded onto PEG segments in a PEG-b-poly(propylene glycol) (PPG)-b-PEG triblock copolymer (Pluronic) chain capped with bulky end groups. Some of the PRx-PEG-$SO_{3}$ demonstrated a higher anticoagulant activity in case of PRx-PEG-$SO_{3}$ (P 105), and compared with the control they showed a lower fibrinogen adsorption in PRx-PEG-$SO_{3}$ (F68) and a higher binding affinity with fibroblast growth factor. The obtained results suggested that polyrotaxane incorporated with PEG-$SO_{3}$ may be applicable to the surface modification of clinically used polymers, especially for blood/cell compatible medical devices.