For bio-electrodes implanted in deep brain, electrode materials will affect the fibrous encapsulation formed on the interface of bio-electrodes and brain tissue which would reduce the operating effect of the bio-electrodes. To reduce or eliminate the fibrous encapsulation layer, N2/H2 plasma treatment process is used to modify the polyurethane which is the most materials of the bio-electrode. The amino groups are produced on the polyurethane surface. After these amino groups have a polymerization reaction with the polypeptide molecule, a layer of the polypeptide molecule is formed on the polyurethane surface of the bio-electrode. These modified bio-electrodes are implanted in the deep brain of the rats for two weeks to observe the immune response and the morphology of the cells on the interface of the bio-electrodes. The results of the experiments indicate that the polypeptide molecules on the polyurethane can improve the immune response of the cells and affect the growth of the fibrous encapsulation on the interface of the bio-electrodes.