A series of poly(dimethylsiloxane) (PDMS)-4,4’-diphenylmethanediisocyanate(MDI)-poly(ethylene glycol) (PEG) multiblock copolymers were synthesized by employing two-step growth polymerization and investigated by AFM, XPS, contact angle system, protein adsorption and platelets adhesion measurements, respectively. It was found that as the molecular weight of PDMS increased, the surface of copolymers had increasing phase separation, while the increase in the molecular weight of PEG decreased the phase separation extents of the copolymer surface. XPS and contact angle measurements showed that the greater the phase separation extent was, the lower both the surface enrichment of PDMS and the surface free energy of the copolymer film were. The protein adsorption experiments indicated that the best phase separation did not exhibit the best biocompatibility.