The surface modification of the polydimethylsiloxane (PDMS) elastomer was studied to obtain a durable hydrophilic surface leading to the reduction in surface tension with an aqueous solution for microflow channel application. Among hydrophilic polymers, it was found that a zwitterionic polymer, sulfobetaine, was adsorbed strongly on the PDMS surface treated with air plasma to afford a durable hydrophilic surface. The PDMS surface treated with air plasma is known to be a silica-like surface with negative charges, and electrostatic interaction, namely, polyion complex interaction between the sulfobetaine polymer and the treated PDMS surface, was sufficiently strong to maintain hydrophilicity even after heat treatment. Furthermore, cell culture experiments showed that the influence of the sulfobetaine polymer on cell growth was negligible, similar to 2-methacryloyloxyethyl phosphoryl choline (MPC) polymer, which is a common polymer for biomedical applications. The AFM observation of the PDMS surface modified with the sulfobetaine polymer suggests that the thickness of the sulfobetaine polymer film was very small on nm order; therefore, this modification method can maintain the microflow channel form. These results demonstrated that the sulfobetaine polymer could be a promising material for the surface modification of PDMS microflow channels for biomedical applications.