The invention relates to a blood compatible polymer layer and a preparation method thereof. Under the condition of ultraviolet irradiation, 6-acrylamide aminocaproic acid and N-vinyl pyrrolidone are initiated to be subjected to a copolymerization reaction on the surface of a silanized substrate, and the blood compatible polymer layer is prepared; and the water contact angle of the prepared blood compatible polymer layer is 40-45 degrees. After the surface of the silanized substrate is grafted with the blood compatible polymer layer, the BSA and Fib protein adsorption amounts are respectively reduced by 75-80% and 60-68%, and no obvious adhesion phenomenon is observed on an erythrocyte adhesion test picture and a platelet adhesion test picture by adopting a laser confocal microscopy test. According to the invention, ultraviolet light is utilized to initiate copolymerization of AACA and NVP monomers, the blood compatible polymer layer with hydrophilic-hydrophobic balance capability is introduced to the surface of the substrate, the operation is simple, the reaction process is controllable, the method is clean and pollution-free, and large-scale production can be realized; and the prepared blood compatible polymer layer has excellent protein adsorption resistance, erythrocyte adhesion resistance and platelet adhesion resistance.