The microwave plasma surface modification of silicone elastomer with allylamine was studied to improve the biocompatibility of the material. An effort was made to clarify the relationships among plasma conditions and surface chemical composition, physical surface properties and biocompatibility of material, as well as the stability of plasma deposited layers. ATR-IR, XPS, Ellipsometry measurements, and contact angle measurements were used to investigate the changes of surface. The stability of plasma-treated silicone surfaces were also studied. The results demonstrated that the temperature and pressure had a strong influence on the chemical composition and structure of surface-deposited layer. The layer was nearly completely crosslinking when the modification was carried out at 60°C. The polymerization speed decreased linearly with temperature. The XPS analysis results showed that the nitrogen element content in the surface layer was very high, especially under low pressure. The nitrogen/carbon ratio in the layer even greatly surpassed that of the allylamine monomer. The wettability of the silicone surface was greatly improved after plasma modification, and increased with the quantities of amine groups. The plasma-treated surfaces have good storage stability in air up to 3 months. The wettability of the surfaces decreased incipiently and then it dramatically increased with further time. The human skin fibroblasts were used to evaluate biocompatibility of plasma-treated silicone elastomer. The surface biocompatibility was greatly improved after modification; human skin fibroblasts adhered quickly and grew well on the modified silicone surface.