A composite structure with high pressure resistance that is suitable for a flow channel is produced by reducing the number of components while maintaining the excellent chemical resistance and high stress tolerance inherent to a glass substrate and a resin substrate. A glass substrate surface is modified with a hydrolyzable silicon compound, and the glass substrate is brought into contact with the resin substrate. Subsequently, the contact surface between the glass substrate and the resin substrate is heated to a temperature from the glass transition temperature to the pyrolysis temperature of the resin substrate, eliminating gaps between the glass substrate and the resin substrate to bring them into close contact with each other, and causing chemical binding or anchor effects between the glass substrate and the resin substrate via the hydrolyzable silicon compound. Thus, the glass substrate and the resin substrate are firmly fixed to each other.