Hydrogels with interpenetrating network (IPN) can overcome thermodynamic incompatibility and obtain transparent materials with limited phase separation. In this report, hydroxyl-grafting polysiloxane (HPSO) was synthesized and transparent silicone hydrogels with interpenetrating network were simultaneously prepared based on radical polymerization of methacrylic monomer of 3-methacryloxypropyl tris(trimethylsiloxy)silane/N,N-dimethylacrylamide and addition polymerization of HPSO/isophorone diisocyanate. The silicone hydrogels were characterized by dehydration kinetics, tensile tester, light transmittance, ion permeability, oxygen permeability, and lysozyme deposition. The results show that increasing the proportion of hydrophobic network of HPSO in the IPN silicone hydrogel decreases equilibrium swelling ratio, ion permeability, Young's modulus, and lysozyme deposition; on the contrary, increased tensile strength, elongation at break and oxygen permeability. Puerarin and ketoconazole were used as models to evaluate the drug loading and in vitro release behavior of the silicone hydrogels. It is revealed that the amount of loaded drugs in the hydrogel decreases with the increase of HPSO network in the hydrogels. All the silicone hydrogels exhibit extended release behavior, especially for ketoconazole, the in vitro release is divided into two phases corresponding to the rapid release at initial 24 h and relatively slow release from 125 to 360 h.