Chitosan (CS)/heparin (HEP) polyelectrolyte complex (PEC) was covalently immobilized onto the surface of polyacrylonitrile (PAN) membrane. The effect of surface modification on the protein adsorption and platelet adhesion, metabolites permeation and anticoagulation activity of the resulting membrane was investigated. Surface characterization such as water contact angle, and X-ray photoelectron spectroscope were performed. The immobilization of PEC caused the water contact angle to reduce, thereby indicating the increase in the hydrophilicity. Protein adsorption, platelet adhesion, and thrombus formation were all reduced by the immobilization of HEP. Anticoagulant activity was evaluated with activated partial thrombin time (APTT), prothrombin time (PT), fibrinogen time, and thrombin time (TT). The results revealed that PEC-immobilizing membrane can improve antithrombogenicity of PAN membrane. In addition, the PEC-immobilized membranes can suppress the proliferation of Pseudomonas aeruginosa. In vitro cytotoxicity test showed leachable substance released was below cytotoxic level. The pure water permeability results show little variation due to PEC-immobilization. Thus PEC-immobilization can endow the PAN membrane hemocompatibility and antibacterial activity while retaining the original permeability.