Polydimethylsiloxane (PDMS) is a biocompatible polymer that has been applied in many fields. However, the surface hydrophobicity of PDMS can limit successful implementation, and this must be reduced by surface modification to improve biocompatibility. In this study, we modified the PDMS surface with a hydrogel and investigated the effect of this on hydrophilicity, bacterial adhesion, cell viability, immune response, and biocompatibility of PDMS. Hydrogels were created from hyaluronic acid and gelatin using a Schiff-base reaction. The PDMS surface and hydrogel were characterized using nuclear magnetic resonance, X-ray photoelectron spectroscopy, attenuated total reflection Fourier-transform infrared spectroscopy, and scanning electron microscopy. The hydrophilicity of the surface was confirmed via a decrease in the water contact angle. Bacterial anti-adhesion was demonstrated for Pseudomonas aeruginosa, Ralstonia pickettii, and Staphylococcus epidermidis, and viability and improved distribution of human-derived adipose stem cells were also confirmed. Decreased capsular tissue responses were observed in vivo with looser collagen distribution and reduced cytokine expression on the hydrogel-coated surface. Hydrogel coating on treated PDMS is a promising method to improve the surface hydrophilicity and biocompatibility for surface modification of biomedical applications.