Three series of multicomponent silicone hydrogels were prepared by the copolymerization of two hydrophobic silicon monomers bis(trimethylsilyloxy) methylsilylpropyl glycerol methacrylate (SiMA) and tris(trimethylsiloxy) 3-methacryloxypropylsilane (TRIS) with three hydrophilic monomers. The surface hydrophilicity of the silicone hydrogels was characterized by contact angle measurements, and an interesting phenomenon was found that the silicone hydrogels made from less hydrophobic monomer SiMA possess more hydrophobic surfaces than those made from TRIS. The surface properties such as morphology and elemental composition of the silicone hydrogels were explored by scanning electron microscopy (SEM) imaging and energy dispersive spectrometry (EDS) analysis, and their relationships with the surface hydrophilicity were investigated in details. The results show neither the surface morphology nor the elemental composition has obvious impact on the surface hydrophilicity. Atomic force microscopy (AFM) imaging revealed that SiMA hydrogel had a more significant phase separation structure, which also made its surface uneven: a lot of tiny holes were observed on the surface. This surface phase separation structure made SiMA hydrogel more difficult to be wetted by water or PBS buffer, i.e., more hydrophobic than TRIS hydrogel. On the basis of these results, we propose that the phase separation structure as well as the nature of silicon monomers might be the fundamental reasons of surface hydrophilicity. These results could help to design a silicone hydrogel with better surface properties and wider application.